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At least 451 records · Page 25

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DOE OSTI2021

Diagenetic formation of uranium-silica polymers in lake sediments over 3,300 years

Significance Understanding the long-term fate of widespread noncrystalline uranium (U) species is critical to improving our knowledge of U biogeochemistry and U-contaminated environments. We use naturally U-enriched lake sediments that have been deposited for thousands of years as an analogue for the progressive evolution of contaminated environments, in order to uncover if noncrystalline species may evolve into more resistant crystalline phases. We combine multidisciplinary tools including U isotope ratio and speciation techniques to describe a mineralogical transformation where organic-bound U evolves into polymeric and nanocrystalline uranium-silica phases that are still easily remobilized even 3,300 y after their deposition. These findings bring an interpretation that illuminates an active debate on uranium mobility in the environment.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2021

Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Marine dissolved organic matter, which originates from phytoplankton, holds as much carbon as Earth’s atmosphere; yet, the biological processes governing its fate are primarily studied under idealized laboratory conditions or through indirect measures such as genome sequencing. In this work, we used isotope labeling to directly quantify uptake of complex carbon pools from the two primary sources of marine organic carbon (diatoms and cyanobacteria) by a natural microbial community. Furthermore, our data show that carbon pools are partitioned into distinct microbial lineages whose physiological properties and resource acquisition strategies match the chemical nature of their preferred substrates. Our results provide ecological and functional insights into the patterns of microbial community structure changes that occur during marine phytoplankton blooms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C $\bar{β}$ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling

Significance Soil organic matter contains a large fraction of global C whose fate is largely governed by soil microbial communities. Global C-cycle models can be improved using information about microbial processes in soil, but the inner workings of soil communities remain largely hidden from view. We used stable isotopes to characterize the guild structure of soil bacteria based on how they assimilated C from different sources. Guild structure corresponded with growth dynamics and rrn copy number. We also show that this guild structure explains microbial biogeographical patterns at continental and global scales. These results suggest that microbial contributions to soil C cycling are largely governed by an anabolic process that governs energy allocation to growth, competition, and survival.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Impact of crowding on the diversity of expanding populations

Crowding effects critically impact the self-organization of densely packed cellular assemblies, such as biofilms, solid tumors, and developing tissues. When cells grow and divide, they push each other apart, remodeling the structure and extent of the population’s range. Recent work has shown that crowding has a strong impact on the strength of natural selection. However, the impact of crowding on neutral processes, which controls the fate of new variants as long as they are rare, remains unclear. Here, we quantify the genetic diversity of expanding microbial colonies and uncover signatures of crowding in the site frequency spectrum. By combining Luria–Delbrück fluctuation tests, lineage tracing in a novel microfluidic incubator, cell-based simulations, and theoretical modeling, we find that the majority of mutations arise behind the expanding frontier, giving rise to clones that are mechanically “pushed out” of the growing region by the proliferating cells in front. These excluded-volume interactions result in a clone-size distribution that solely depends on where the mutation first arose relative to the front and is characterized by a simple power law for low-frequency clones. Our model predicts that the distribution depends on a single parameter—the characteristic growth layer thickness—and hence allows estimation of the mutation rate in a variety of crowded cellular populations. Combined with previous studies on high-frequency mutations, our finding provides a unified picture of the genetic diversity in expanding populations over the whole frequency range and suggests a practical method to assess growth dynamics by sequencing populations across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells

The superior photosynthetic efficiency of C 4 leaves over C 3 leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A species’ response to spatial climatic variation does not predict its response to climate change

The dominant paradigm for assessing ecological responses to climate change assumes that future states of individuals and populations can be predicted by current, species-wide performance variation across spatial climatic gradients. However, if the fates of ecological systems are better predicted by past responses to in situ climatic variation through time, this current analytical paradigm may be severely misleading. Empirically testing whether spatial or temporal climate responses better predict how species respond to climate change has been elusive, largely due to restrictive data requirements. Here, we leverage a newly collected network of ponderosa pine tree-ring time series to test whether statistically inferred responses to spatial versus temporal climatic variation better predict how trees have responded to recent climate change. When compared to observed tree growth responses to climate change since 1980, predictions derived from spatial climatic variation were wrong in both magnitude and direction. This was not the case for predictions derived from climatic variation through time, which were able to replicate observed responses well. Future climate scenarios through the end of the 21st century exacerbated these disparities. These results suggest that the currently dominant paradigm of forecasting the ecological impacts of climate change based on spatial climatic variation may be severely misleading over decadal to centennial timescales.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Nr2f1 enhancers have distinct functions in controlling Nr2f1 expression during cortical development

There is evidence that transcription factor (TF) encoding genes, which temporally control development in multiple cell types, can have tens of enhancers that regulate their expression. The NR2F1 TF developmentally promotes caudal and ventral cortical regional fates. Here, we epigenomically compared the activity of Nr2f1’s enhancers during mouse cortical development with their activity in a transgenic assay. We identified at least six that are likely to be important in prenatal cortical development, with three harboring de novo mutants identified in ASD individuals. We chose to study the function of two of the most robust enhancers by deleting them singly or together. We found that they have distinct and overlapping functions in driving Nr2f1’s regional and laminar expression in the developing cortex. Thus, these two enhancers, probably in combination with the others that we defined epigenetically, precisely tune Nr2f1’s regional, cell type, and temporal expression during corticogenesis.

Liu, Zhidong↗

DOE OSTI2025

Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus

Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N 2 O) emissions, although biochemical origins of this N 2 O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus . We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH 2 OH) to dioxygen (O 2 ) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N 2 via reaction with NH 2 OH and dimerization with itself to yield N 2 O. These results afford one plausible enzymatic origin for N 2 O release by AOA. Moreover, these results reveal a physiologically relevant enzymatic reaction for producing HNO, an enigmatic nitrogen oxide speculated to be operative in cellular signaling and in energy transduction.

Voland, Robert W. (ORCID:0000000201061257)↗

DOE OSTI2025

Observed declines in leaf nitrogen explained by photosynthetic acclimation to CO 2

Widespread evidence of decreasing leaf nutrients has raised concerns about ecosystem productivity under global change. Interpreting trends in leaf nutrients has important implications for the fate of ecosystem services, particularly the role of forests in mitigating climate change and sustaining quality food sources. Here, we challenge the common interpretation that decreasing leaf nitrogen concentration (LNC) is evidence of increasing nutrient limitations on ecosystem primary productivity. Instead, we show that declines in LNC (4% decrease per 50 ppm CO 2 increase), observed across 409 European forest plots over 22 y, can be explained by reduced photosynthetic nitrogen demand. This regional trend is consistent with leaf acclimation to increasing atmospheric CO 2 according to optimality theory. This finding suggests that enhanced photosynthetic nitrogen use efficiency due to CO 2 fertilization may lead to less nitrogen uptake and/or reallocation of nitrogen for plant growth and other functions. Our results have large implications for understanding and simulating interactions between ecosystem nitrogen and carbon cycles and suggest nitrogen requirements for terrestrial carbon uptake under elevated CO 2 may be lower than previously thought.

CO2 fertilization↗

DOE OSTI2022

Catalytic Effects of Silver in Iodine Reactors for Dissolved Used Nuclear Fuel

The dissolution of used nuclear fuel generates a variety of off-gasses including flammable hydrogen and other species that are a concern for environmental release. The H-Canyon facility at the Savannah River Site is currently dissolving aluminum-clad research reactor fuel from material test reactors and the High Flux Isotope Reactor (HFIR) using a mercury-catalyzed nitric acid flowsheet. Savannah River National Laboratory recently developed and deployed a Raman spectrometer to monitor the off-gas stream from the dissolution process. Results from these measurements indicated a lack of the expected hydrogen, nitrous oxide, and nitric oxide in the off-gas stream. It was proposed that the silver on the silver nitrate–coated berl saddles present in the reactors for iodine capture were acting as a catalytic hydrogen recombiner. Nitric oxide is readily oxidized to nitrogen dioxide under normal conditions, but it was unclear what happened to the nitrous oxide. A laboratory-scale iodine reactor was assembled and filled with silver nitrate–coated berl saddles to help ascertain the fate of nitrous oxide and hydrogen. Testing with this laboratory-scale reactor observed the recombination of hydrogen when a simulated dissolver off-gas was passed through the reactor containing silver nitrate–coated berl saddles at the approximate temperatures seen in H-Canyon. However, the nitrous oxide concentration was unchanged, suggesting a more complex process occurring within the off-gas stream before it reaches the iodine reactors at H-Canyon.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Droplet and Particle Methods to Investigate Turbulent Particle Laden Jets

The SARS-CoV-2 pandemic has heightened the interest in particle-laden turbulent jets generated by breathing, talking, coughing and sneezing, and how these can contribute to disease transmission. We present quantitative measurement methods for such flows, while exploring and offering improvements for common shortcomings. We generate jets consisting of either liquid droplets or solid particles in an isothermal, quiescent and electrically isopotential experimental chamber that was constructed to control the effects of ambient forcing on jet behavior. For liquid droplets, we find promise in surface deposition analysis based on fluorescent tracer use. For particles, we explore the performance of commercially available adhesive sampling strips and develop conductive grounded carbon tape based sampling strips. We explore ways in which the smallest of thermal gradients or electrostatic charge issues can affect particle dispersion, and suggest practical methods to address these issues. The developed methods are applied to study the simultaneous deposition of (Formula presented.) 25, 50 and 200 μm solid particles from a particle laden turbulent jet with a mean velocity of 33.2 m/s. The deposition location as a function of particle size was compared to results from a simple numerical RANS model, and illustrates ways in which imprecise initial or boundary conditions can lead to a notable deviation from experimental results. The differences in deposition pattern seen in experimental and numerical results despite a carefully controlled environment and characterized particle ejection indicate the need for a more stringent numerical model validation, especially when studying fate and transport of mid-range (neither purely aerosol or ballistic) sized particles.

42 ENGINEERING↗

DOE OSTI2021

Transport and chemistry of isoprene and its oxidation products in deep convective clouds

Deep convective clouds can transport trace gases from the planetary boundary layer into the upper troposphere where subsequent chemistry may impact aerosol particle formation and growth. In this modelling study, we investigate processes that affect isoprene and its oxidation products injected into the upper troposphere by an isolated deep convective cloud in the Amazon. We run a photochemical box model with coupled cloud microphysics along hundreds of individual air parcel trajectories sampled from a cloud-resolving model simulation of a convective event. The box model simulates gas-phase chemical reactions, gas scavenging by liquid and ice hydrometeors, and turbulent dilution inside a deep convective cloud. The results illustrate the potential importance of gas uptake to anvil ice in regulating the intensity of the isoprene oxidation and associated low volatility organic vapour concentrations in the outflow. Isoprene transport and fate also depends on the abundance of lightning-generated nitrogen oxide radicals (NO x = NO + NO 2 ). If gas uptake on ice is efficient and lightning activity is low, around 30% of the boundary layer isoprene will survive to the cloud outflow after approximately one hour of transport, while all the low volatile oxidation products will be scavenged by the cloud hydrometeors. If lightning NO x is abundant and gas uptake by ice is inefficient, then all isoprene will be oxidised during transport or in the immediate outflow region, while several low volatility isoprene oxidation products will have elevated concentrations in the cloud outflow. Reducing uncertainties associated with the uptake of vapours on ice hydrometeors, especially HO 2 and oxygenated organics, is essential to improve predictions of isoprene and its oxidation products in deep convective outflows and their potential contribution to new particle formation and growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Quantifying airborne fraction trends and the destination of anthropogenic CO 2 by tracking carbon flows in a simple climate model

Abstract Atmospheric carbon dioxide (CO 2 ) concentrations have increased as a direct result of human activity and are at their highest level over the last 2 million years, with profound impacts on the Earth system. However, the magnitude and future dynamics of land and ocean carbon sinks are not well understood; therefore, the amount of anthropogenic fossil fuel emissions that remain in the atmosphere (the airborne fraction) is poorly constrained. This work aims to quantify the sources and controls of atmospheric CO 2 , the fate of anthropogenic CO 2 over time, and the likelihood of a trend in the airborne fraction. We use Hector v3.0, a coupled simple climate and carbon cycle model with the novel ability to explicitly track carbon as it flows through the Earth system. We use key model parameters in a Monte Carlo analysis of 15 000 model runs from 1750 to 2300. Results are filtered for physical realism against historical observations and CMIP6 projection data, and we calculate the relative importance of parameters controlling how much anthropogenic carbon ends up in the atmosphere. Modeled airborne fraction was roughly 52%, consistent with observational studies. The overwhelming majority of model runs exhibited a negative trend in the airborne fraction from 1960–2020, implying that current-day land and ocean sinks are proportionally taking up more carbon than the atmosphere. However, the percentage of atmospheric CO 2 derived from anthropogenic origins can be much higher because of Earth system feedbacks. We find it peaks at over 90% between 2010–2050. Moreover, when looking at the destination of anthropogenic fossil fuel emissions, only a quarter ends up in the atmosphere while more than half of emissions are taken up by the land sink on centennial timescales. This study evaluates the likelihood of airborne fraction trends and provides insights into the dynamics of anthropogenic CO 2 in the Earth system.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Climate-Mediated Changes to Linked Terrestrial and Marine Ecosystems across the Northeast Pacific Coastal Temperate Rainforest Margin

Coastal margins are important areas of materials flux that link terrestrial and marine ecosystems. Consequently, climate-mediated changes to coastal terrestrial ecosystems and hydrologic regimes have high potential to influence nearshore ocean chemistry and food web dynamics. Research from tightly coupled, high-flux coastal ecosystems can advance understanding of terrestrial–marine links and climate sensitivities more generally. In the present article, we use the northeast Pacific coastal temperate rainforest as a model system to evaluate such links. We focus on key above- and belowground production and hydrological transport processes that control the land-to-ocean flow of materials and their influence on nearshore marine ecosystems. We evaluate how these connections may be altered by global climate change and we identify knowledge gaps in our understanding of the source, transport, and fate of terrestrial materials along this coastal margin. Finally, we propose five priority research themes in this region that are relevant for understanding coastal ecosystem links more broadly.

temperate rainforest, coastal margin, climate chan↗

DOE OSTI2020

Post-Transcriptional Mechanisms Respond Rapidly to Ecologically Relevant Thermal Fluctuations During Temperature-Dependent Sex Determination

An organism’s ability to integrate transient environmental cues experienced during development into molecular and physiological responses forms the basis for adaptive shifts in phenotypic trajectories. During temperature-dependent sex determination (TSD), thermal cues during discrete periods in development coordinate molecular changes that ultimately dictate sexual fate and contribute to patterns of inter- and intra-sexual variation. How these mechanisms interface with dynamic thermal environments in nature remain largely unknown. By deploying thermal loggers in wild nests of the American alligator (Alligator mississippiensis) over two consecutive breeding seasons, we observed that 80% of nests exhibit both male- and female-promoting thermal cues during the thermosensitive period, and of these nests, all exhibited both male- and female-promoting temperatures within the span of a single day. These observations raise a critical question—how are opposing environmental cues integrated into sexually dimorphic transcriptional programs across short temporal scales? To address this question, alligator embryos were exposed to fluctuating temperatures based on nest thermal profiles and sampled over the course of a daily thermal fluctuation. We examined the expression dynamics of upstream genes in the temperature-sensing pathway and find that post-transcriptional alternative splicing and transcript abundance of epigenetic modifier genes JARID2 and KDM6B respond rapidly to thermal fluctuations while transcriptional changes of downstream effector genes, SOX9 and DMRT1, occur on a delayed timescale. Our findings reveal how the basic mechanisms of TSD operate in an ecologically relevant context. We present a hypothetical hierarchical model based on our findings as well as previous studies, in which temperature-sensitive alternative splicing incrementally influences the epigenetic landscape to affect the transcriptional activity of key sex-determining genes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The role of supernova convection for the lower mass gap in the isolated binary formation of gravitational wave sources

ABSTRACT Understanding the astrophysical phenomena involving compact objects requires an insight about the engine behind the core-collapse supernovae (SNe) and the fate of the stellar collapse of massive stars. In particular, this insight is crucial in developing an understanding of the origin and formation channels of the growing populations of the detected black hole–black hole, black hole–neutron star, and neutron star–neutron star mergers. The time-scale of convection growth may have a large effect on the strength of SN explosion and therefore also on the mass distribution of stellar remnants. We adopt new formulas for the relation between the pre-SN star properties and their remnants and check how they impact the population of double compact object (DCO) mergers formed via the isolated binary evolution. The new formulas give one the ability to test a wide spectrum of assumptions on the convection growth time. In particular, the different variants allow for a smooth transition between having a deep mass gap and a remnant mass distribution filled by massive neutron stars and low-mass black holes. We present the distribution of masses, mass ratios, and the local merger rate densities of DCO for the different variants of new formulas and test them together with different approaches to other highly uncertain processes. We find that the mass distribution of DCO mergers is sensitive to the adopted assumption on the SN convection growth time-scale up to $m_1+m_2 \lesssim 35 \, \mathrm{M}_{\odot }$. Between the two extreme tested variants the probability of compact object formation within the mass gap may differ by up to approximately two orders of magnitude.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

The end game(s) of photosynthetic carbon metabolism

Abstract The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms use the reaction sequence described 70 yrs ago, which is now known as the Calvin–Benson cycle or variants such as the Calvin–Benson–Bassham cycle or Benson–Calvin cycle. However, once the carbon has entered the Calvin–Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin–Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.

59 BASIC BIOLOGICAL SCIENCES↗