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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

X-ray Linear Dichroism in Apatite

The recent observation in parrotfish teeth of X-ray linear dichroism motivated an in-depth investigation into this spectroscopic effect in various apatite crystals, including geologic hydroxyapatite (Ca 5 (PO 4 ) 3 OH), fluorapatite (Ca 5 (PO 4 ) 3 F), and their biogenic counterparts in human bone, mouse enamel, and in parrotfish bone, dentin, and enameloid, the equivalent of dental enamel in certain fish. These data are important because they now enable visualization of the nano- to microscale structure of apatite crystals in teeth and bone. Polarization-dependent imaging contrast (PIC) maps of lamellar bone, obtained with a new method that minimizes space-charge and charging effects, show the expected rotating apatite crystal orientations. PIC maps of mouse enamel reveal a complex arrangement of hydroxyapatite crystals perpendicular to the dentin-enamel junction, with rods arranged in a decussation pattern in inner enamel and nearly parallel to one another in outer enamel. In both inner and outer enamel crystal c-axes are not always aligned with the rod elongation direction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Analysis of Hypoxia and Sensitivity to Nutrient Pollution in Salish Sea

We report that increasing levels of nutrients, persistent hypoxia, harmful algal blooms, and increased frequency of fish kills are degrading the ecological health of the Salish Sea. An improved version of a diagnostic hydrodynamic and biogeochemical model (nutrients, phytoplankton, carbon, dissolved oxygen, pH) of the Salish Sea has been developed with the ability to simulate characteristic circulation and water quality features. Sensitivity tests were conducted to assess the responsiveness of the system to land-based (rivers and wastewater sources) nutrient loading. The influence of Fraser River on the magnitude of estuarine exchange with the Pacific Ocean and nearshore habitat was examined given that it contributes nearly half of the total freshwater discharged to the Salish Sea. A large region of hypoxia in Hood Canal that extends over 30–40 km during its peak was reproduced and attributed primarily to the existence of a two-layer classic fjord-type circulation and a nearly stagnant deep bottom layer that occupies nearly 60% of the water column. Nitrate mass in the euphotic zone from land-based and oceanic sources is depleted to near-zero limiting levels during summer. Under such conditions, the Salish Sea is responsive to changes in nutrient loads entering the euphotic zone directly. Lastly, a hypothetical scenario involving the elimination of land-based nutrient sources results in notable water-quality improvement, featuring a reduction in algal biomass (≈5.4%), reduction in sediment oxygen demand (≈17.1%), and significant reduction in hypoxic area (≈39%) and exposure in area-days to bottom layer hypoxia (≈62%) within the Salish Sea.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

How Much Water Is Evaporated Across California? A Multiyear Assessment Using a Biophysical Model Forced With Satellite Remote Sensing Data

Abstract California is expected to experience great spatial/temporal variations evaporation. These variations arise from strong north‐south, east‐west gradients in rainfall and vegetation, strong interannual variability in rainfall (±30%) and strong seasonal variability in the supply and demand for moisture. We used the Breathing Earth System Simulator to evaluate the rates and sums of evaporation across California, over the 2001–2017 period. Breathing Earth System Simulator is a bottom‐up, biophysical model that couples subroutines that calculate the surface energy balance, photosynthesis, and stomatal conductance. The model is forced with high‐resolution remote sensing data (1 km).The questions we address are as follows: How much water is evaporated across the natural and managed ecosystems of California? How much does evaporation vary during the booms and busts in annual rainfall? and Is evaporation increasing with time due to a warming climate? Mean annual evaporation, averaged over the 2001–2017 period, was relatively steady (393 ± 21 mm/year) given the high interannual variation in precipitation (519 ± 140 mm/year). No significant trend in evaporation at the statewide level was detected over this time period, despite a background of a warming climate. Irrigated agricultural crops and orchards, at 1‐km scale, use less water than inferred estimates for individual fields. This leaves the potential for sharing water, a scarce resource, more equitably among competing stakeholders, for example, farms, fish, people, and ecosystems.

Baldocchi, Dennis↗
DOE OSTI2017

Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma

Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, we present the largest sequencing study of osteosarcoma to date, comprising 112 childhood and adult tumours encompassing all major histological subtypes. A key finding of our study is the identification of mutations in insulin-like growth factor (IGF) signalling genes in 8/112 (7%) of cases. We validate this observation using fluorescence in situ hybridization (FISH) in an additional 87 osteosarcomas, with IGF1 receptor (IGF1R) amplification observed in 14% of tumours. These findings may inform patient selection in future trials of IGF1R inhibitors in osteosarcoma. Analysing patterns of mutation, we identify distinct rearrangement profiles including a process characterized by chromothripsis and amplification. This process operates recurrently at discrete genomic regions and generates driver mutations. Lastly, it may represent an age-independent mutational mechanism that contributes to the development of osteosarcoma in children and adults alike.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood. Diet appears to be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique gut microbiomes with surprising parallels in functional capacity and higher level taxonomy to those of terrestrial herbivores. These similarities likely reflect a shared role for fermentative metabolisms despite a shift in primary carbon sources from plant-derived to animal-derived polysaccharides, such as chitin. In contrast, protein catabolism and essential amino acid synthesis pathways in baleen whale microbiomes more closely resemble those of terrestrial carnivores. Our results demonstrate that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Hydrodynamic schooling of flapping swimmers

Fish schools and bird flocks are fascinating examples of collective behaviours in which many individuals generate and interact with complex flows. Motivated by animal groups on the move, here we explore how the locomotion of many bodies emerges from their flow-mediated interactions. Through experiments and simulations of arrays of flapping wings that propel within a collective wake, we discover distinct modes characterized by the group swimming speed and the spatial phase shift between trajectories of neighbouring wings. For identical flapping motions, slow and fast modes coexist and correspond to constructive and destructive wing–wake interactions. Simulations show that swimming in a group can enhance speed and save power, and we capture the key phenomena in a mathematical model based on memory or the storage and recollection of information in the flow field. Lastly, these results also show that fluid dynamic interactions alone are sufficient to generate coherent collective locomotion, and thus might suggest new ways to characterize the role of flows in animal groups.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir

Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016–2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities

Abstract Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150–500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.

09 BIOMASS FUELS↗
DOE OSTI2019

Schools of skyrmions with electrically tunable elastic interactions

Coexistence of order and fluidity in soft matter often mimics that in biology, allowing for complex dynamics and applications-like displays. In active soft matter, emergent order can arise because of such dynamics. Powered by local energy conversion, this behavior resembles motions in living systems, like schooling of fish. Similar dynamics at cellular levels drive biological processes and generate macroscopic work. Inanimate particles capable of such emergent behavior could power nanomachines, but most active systems have biological origins. Here we show that thousands-to-millions of topological solitons, dubbed “skyrmions”, while each converting macroscopically-supplied electric energy, exhibit collective motions along spontaneously-chosen directions uncorrelated with the direction of electric field. Within these “schools” of skyrmions, we uncover polar ordering, reconfigurable multi-skyrmion clustering and large-scale cohesion mediated by out-of-equilibrium elastic interactions. Remarkably, this behavior arises under conditions similar to those in liquid crystal displays and may enable dynamic materials with strong emergent electro-optic responses.

Science & Technology - Other Topics↗
DOE OSTI2022

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Trace metals have been an important ingredient for life throughout Earth’s history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Conserved enhancers control notochord expression of vertebrate Brachyury

The cell type-specific expression of key transcription factors is central to development and disease. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three conserved Brachyury-controlling notochord enhancers, T3, C, and I, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, in cis deletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The three Brachyury-driving notochord enhancers are conserved beyond mammals in the brachyury/tbxtb loci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers for Brachyury/T/TBXTB notochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Severe 21st-century ocean acidification in Antarctic Marine Protected Areas

Antarctic coastal waters are home to several established or proposed Marine Protected Areas (MPAs) supporting exceptional biodiversity. Despite being threatened by anthropogenic climate change, uncertainties remain surrounding the future ocean acidification (OA) of these waters. Here we present 21st-century projections of OA in Antarctic MPAs under four emission scenarios using a high-resolution ocean–sea ice–biogeochemistry model with realistic ice-shelf geometry. By 2100, we project pH declines of up to 0.36 (total scale) for the top 200 m. Vigorous vertical mixing of anthropogenic carbon produces severe OA throughout the water column in coastal waters of proposed and existing MPAs. Consequently, end-of-century aragonite undersaturation is ubiquitous under the three highest emission scenarios. Given the cumulative threat to marine ecosystems by environmental change and activities such as fishing, our findings call for strong emission-mitigation efforts and further management strategies to reduce pressures on ecosystems, such as the continuation and expansion of Antarctic MPAs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Branched-chain amino acid specialization drove diversification within Calditenuaceae ( Caldarchaeia ) and enables their cultivation

Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 6 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.

Biological and medical sciences↗
DOE OSTI2023

The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins—including gene expression, chromatin occupancy and three-dimensional conformation—we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolution of neuronal cell classes and types in the vertebrate retina

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CreelCat, a Catalog of United States Inland Creel and Angler Survey Data

The United States Inland Creel and Angler Survey Catalog (CreelCat) contains a national compilation of angler and creel survey data collected by natural resource management agencies across the United States (including Washington, D.C. and Puerto Rico). These surveys are used to help inform the management of recreational fisheries, by collecting information about anglers including what they are catching and harvesting, the amount of effort they expend, their angling preferences, and demographic information. As of May 1, 2023, CreelCat houses over 14,729 surveys from 33 states, Puerto Rico, and Washington, D.C., comprising 235 data fields across 8 tables. These tables contain 235,015 records of fish catch and harvest metrics, 27,250 angler preference metrics, 14,729 records of survey characteristics, 13,576 records of effort metrics, and 409 records of angler demographics. Though individual creel surveys are often deployed to meet local science and management objectives, creel data aggregated across jurisdictions has the potential to address larger scale research and management needs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids

Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Persistent meanders and eddies lead to quasi-steady Lagrangian transport patterns in a weak western boundary current

The Brazil Current (BC) is a weak western boundary current flowing along the Southwestern Atlantic Ocean. It is frequently described as a flow with intense mesoscale activity and relatively low volume transport between 5.0 and 10.0 Sv. We use a 13-year eddy-resolving primitive-equation simulation to show that the presence of persistent meanders and eddies leads to characteristic quasi-steady Lagrangian transport patterns, aptly extracted through climatological Lagrangian Coherent Structures (cLCS). The cLCS position the surface expression of the BC core along the 2000-m isobath, in excellent visual agreement with high resolution satellite sea-surface temperature and the model Eulerian mean velocity. The cLCS deformation pattern also responds to zonally persistent cross-shelf SSH transition from positive (high) values near coastline to low (negative) values between 200- and 2000-m and back to positive (high) offshore from the 2000-m isobath. Zonally-paired cyclonic and anticyclonic structures are embedded in this transition, also causing the cLCS to deform into chevrons. An efficient transport barrier is identified close to the 200-m isobath confirmed by limited inshore movement of drogued drifters and accurately indicated by an along slope maxima of climatological strength of attraction. We also show that the persistent cyclonic and anticyclonic structures may induce localized cross-shelf transport. Regions of low climatological strength of attraction coincide with large shelves and with stagnant synthetic trajectories. We also show that cLCS accurately depict trajectories initiated at the location of Chevron’s spill (November 2011) as compared to synthetic and satellite-tracked trajectories, and the outline of the oil from that accident. There is also an agreement between the large-scale oil slicks reaching the Brazilian beaches (from August 2019 to February 2020) and the strength of climatological attraction at the coast. Our work also clarifies the influence of persistent mesoscale structures on the regional circulation. The identification and quantitative description of climatological Lagrangian coherent structures is expected to improve the effectiveness of future emergency response to oil spills, contingency planning, rescue operations, larval and fish connectivity assessment, drifter launch strategies, waste pollutant and marine debris dispersion and destination.

54 ENVIRONMENTAL SCIENCES↗