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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Abundance and properties of dark radiation from the cosmic microwave background

We study the cosmological signatures of new light relics that are collisionless like standard neutrinos or are strongly interacting. We provide a simple and succinct rephrasing of their physical effects in the cosmic microwave background, as well as the resulting parameter degeneracies with other cosmological parameters, in terms of the total radiation abundance and the fraction thereof that freely streams. In these more general terms, interacting and noninteracting light relics are differentiated by their respective decrease and increase of the free-streaming fraction, and, moreover, the scale-dependent interplay thereof with a common, correlated reduction of the fraction of matter in baryons. We then derive updated constraints on various dark-radiation scenarios with the latest cosmological observations, employing this language to identify the physical origin of the impact of each dataset. The “PR4” reanalyses of Planck CMB data prefer a larger primordial helium yield and therefore also slightly more radiation than the 2018 analysis; we investigate the differences between the two releases that drives these shifts. Smaller free-streaming fractions are disfavored by the excess lensing of the CMB measured in lensing reconstruction data from Planck and the Atacama Cosmology Telescope. On the other hand, baryon acoustic oscillation measurements from the Dark Energy Spectroscopic Instrument drive marginal detections of new, strongly interacting light relics due to that data's preference for lower matter fractions. Finally, we forecast measurements from the CMB-S4 experiment.

cosmological parameters from CMBR↗
DOE OSTI2020

Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes

Differential epidermal growth factor receptor (EGFR) phosphorylation is thought to couple receptor activation to distinct signaling pathways. However, the molecular mechanisms responsible for biased signaling are unresolved due to a lack of insight into the phosphorylation patterns of full-length EGFR. We extended a single-molecule pull-down technique previously used to study protein–protein interactions to allow for robust measurement of receptor phosphorylation. We found that EGFR is predominantly phosphorylated at multiple sites, yet phosphorylation at specific tyrosines is variable and only a subset of receptors share phosphorylation at the same site, even with saturating ligand concentrations. We found distinct populations of receptors as soon as 1 min after ligand stimulation, indicating early diversification of function. To understand this heterogeneity, we developed a mathematical model. The model predicted that variations in phosphorylation are dependent on the abundances of signaling partners, while phosphorylation levels are dependent on dimer lifetimes. The predictions were confirmed in studies of cell lines with different expression levels of signaling partners, and in experiments comparing low- and high-affinity ligands and oncogenic EGFR mutants. These results reveal how ligand-regulated receptor dimerization dynamics and adaptor protein concentrations play critical roles in EGFR signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The age–chemical abundance structure of the Galactic disc – II. α -dichotomy and thick disc formation

ABSTRACT We extend our previous work on the age–chemical abundance structure of the Galactic outer disc to the inner disc (4 < r < 8 kpc) based on the SDSS/APOGEE survey. Different from the outer disc, the inner disc stars exhibit a clear bimodal distribution in the [Mg/Fe]–[Fe/H] plane. While a number of scenarios have been proposed in the literature, it remains challenging to recover this bimodal distribution with theoretical models. To this end, we present a chemical evolution model embedding a complex multiphase inner disc formation scenario that matches the observed bimodal [Mg/Fe]–[Fe/H] distribution. In this scenario, the formation of the inner disc is dominated by two main starburst episodes $6\,$Gyr apart with secular, low-level star formation activity in between. In our model, the first starburst occurs at early cosmic times ($t\sim 1\,$ Gyr) and the second one $6\,$ Gyr later at a cosmic time of $t\sim 7\,$ Gyr. Both these starburst episodes are associated with gas accretion events in our model, and are quenched rapidly. The first starburst leads to the formation of the high-α sequence, and the second starburst leads to the formation of the metal-poor low-α sequence. The metal-rich low-α stars, instead, form during the secular evolution phase between the two bursts. Our model shows that the α-dichotomy originates from the rapid suppression of star formation after the first starburst. The two starburst episodes are likely to be responsible for the formation of the geometric thick disc (z >1 kpc), with the old inner thick disc and the young outer thick disc forming during the first and the second starbursts, respectively.

Lian, Jianhui↗
DOE OSTI2022

Model BOSS and eBOSS luminous red galaxies at 0.2< z<1.0 using SubHalo Abundance Matching with three parameters

SubHalo Abundance Matching (SHAM) is an empirical method for constructing galaxy catalogues based on high-resolution N-body simulations. Here, we apply SHAM on the UNIT simulation to simulate SDSS BOSS/eBOSS luminous red galaxies (LRGs) within a wide redshift range of 0.2 < $z$ < 1.0. Besides the typical SHAM scatter parameter σ, we include $v$ smear and V ceil to take into account the redshift uncertainty and the galaxy incompleteness, respectively. These two additional parameters are critical for reproducing the observed 2PCF multipoles on 5–25$\, h^{-1}\, {\rm Mpc}$. The redshift uncertainties obtained from the best-fitting $v$ smear agree with those measured from repeat observations for all SDSS LRGs except for the LOWZ sample. We explore several potential systematics but none of them can explain the discrepancy found in LOWZ. Our explanation is that the LOWZ galaxies might contain another type of galaxies that needs to be treated differently. The evolution of the measured σ and Vceil also reveals that the incompleteness of eBOSS galaxies decreases with the redshift. This is the consequence of the magnitude lower limit applied in eBOSS LRG target selection. Our SHAM also set upper limits for the intrinsic scatter of the galaxy–halo relation, given a complete galaxy sample: σ int < 0.31 for LOWZ at 0.2 < $z$ < 0.33, σ int < 0.36 for LOWZ at 0.33 < $z$ < 0.43, and σ int < 0.46 for CMASS at 0.43 < $z$ < 0.51. The projected 2PCFs of our SHAM galaxies also agree with the observational ones on the 2PCF fitting range.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Abundance matching analysis of the emission-line galaxy sample in the extended Baryon Oscillation Spectroscopic Survey

We present the measurements of the small-scale clustering for the emission-line galaxy (ELG) sample from the extended Baryon Oscillation Spectroscopic Survey (eBOSS) in the Sloan Digital Sky Survey IV (SDSS-IV). We use conditional abundance matching method to interpret the clustering measurements from 0.34 to 70 h -1 Mpc. In order to account for the correlation between properties of ELGs and their environment, we add a secondary connection between star formation rate of ELGs and halo accretion rate. Three parameters are introduced to model the ELG [O II ] luminosity and to mimic the target selection of eBOSS ELGs. The parameters in our models are optimized using Markov Chain Monte Carlo (MCMC) method. We find that by conditionally matching star formation rate of galaxies and the halo accretion rate, we are able to reproduce the eBOSS ELG small-scale clustering within 1σ error level. Our best-fitting model shows that the eBOSS ELG sample only consists of ~ 12 per cent of all star-forming galaxies, and the satellite fraction of eBOSS ELG sample is 19.3 per cent. We show that the effect of assembly bias is ~ 20 per cent on the two-point correlation function and ~ 5 per cent on the void probability function at scale of r ~ 20 h -1 Mpc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

High-Sensitivity rf Detection Using an Optically Pumped Comagnetometer Based on Natural-Abundance Rubidium with Active Ambient-Field Cancellation

To detect a specific radio-frequency (rf) magnetic field, rf optically pumped magnetometers (OPMs) require a static magnetic field to set the Larmor frequency of the atoms equal to the frequency of interest. However, unshielded and variable magnetic field environments (e.g., an rf OPM on a moving platform) pose a problem for rf OPM operation. Here, we demonstrate the use of a natural-abundance rubidium vapor to make a comagnetometer to address this challenge. Our implementation builds upon the simultaneous application of several OPM techniques within the same vapor cell. First, we use a modified implementation of an OPM variometer based on 87 Rb to detect and actively cancel unwanted external fields at frequencies ≲60 Hz using active feedback to a set of field control coils. In this experiment, we exploit this stabilized field environment to implement a high-sensitivity rf magnetometer using 85 Rb. Using this approach, we demonstrate the ability to measure rf fields with a sensitivity of approximately 9 fT Hz -1/2 inside a magnetic shield in the presence of an applied field of approximately 20 μT along three mutually orthogonal directions. This demonstration opens up a path toward completely unshielded operation of a high-sensitivity rf OPM.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Mass measurements of neutron-rich gallium isotopes refine production of nuclei of the first r -process abundance peak in neutron-star merger calculations

We report mass measurements of neutron-rich Ga isotopes 80–85 Ga with TRIUMF's Ion Trap for Atomic and Nuclear science. The measurements determine the masses of 80–83 Ga in good agreement with previous measurements. Here, the masses of 84 Ga and 85 Ga were measured for the first time. Uncertainties between 25 and 48 keV were reached. The new mass values reduce the nuclear uncertainties associated with the production of A ≈ 84 isotopes by the r-process for astrophysical conditions that might be consistent with a binary neutron star (BNS) merger producing a blue kilonova. Our nucleosynthesis simulations confirm that BNS merger may contribute to the first abundance peak under moderate neutron-rich conditions with electron fractions Y e = 0.35–0.38.

59 ≤ A ≤ 89↗
DOE OSTI2020

Spectroscopy of 30 P and the abundance of 29 Si in presolar grains

The astrophysical 29 Si(p,γ) reaction is expected to play a key role in determining the final 29 Si yields ejected in nova explosions. Such yields are used to accurately identify the stellar origins of meteoritic stardust and recently, distinctive silicon isotopic ratios have been extracted from a number of presolar grains. Here, the light-ion 28 Si( 3 He,p) fusion-evaporation reaction was used to populate low-spin proton-unbound excited states in the nucleus 30 P that govern the rate of the astrophysical 29 Si(p,γ) reaction. In particular, γ decays were observed from resonances up to E r = 500keV, and key resonances at 217 and 315 keV have now been identified as 2 + and 2¯ levels, respectively. Here, the present paper provides the first estimate of the 217-keV resonance strength and indicates that the strength of the 315-keV resonance, which dominates the rate of the 29 Si(p,γ) reaction over the entire peak temperature range of oxygen-neon novae, is higher than previously expected. As such, the abundance of 29 Si ejected during nova explosions is likely to be less than that predicted by the most recent theoretical models.

20 ≤ A ≤ 38↗
DOE OSTI2020

Dark Energy Survey Year 1 Results: Cosmological constraints from cluster abundances and weak lensing

In this work we perform a joint analysis of the counts and weak lensing signal of redMaPPer clusters selected from the Dark Energy Survey (DES) Year 1 dataset. Our analysis uses the same shear and source photometric redshifts estimates as were used in the DES combined probes analysis. Our analysis results in surprisingly low values for $S_8 =\sigma_8(\Omega_{\rm m}/0.3)^{0.5}= 0.65\pm 0.04$, driven by a low matter density parameter, $\Omega_{\rm m}=0.179^{+0.031}_{-0.038}$, with $\sigma_8-\Omega_{\rm m}$ posteriors in $2.4\sigma$ tension with the DES Y1 3x2pt results, and in $5.6\sigma$ with the Planck CMB analysis. These results include the impact of post-unblinding changes to the analysis, which did not improve the level of consistency with other data sets compared to the results obtained at the unblinding. The fact that multiple cosmological probes (supernovae, baryon acoustic oscillations, cosmic shear, galaxy clustering and CMB anisotropies), and other galaxy cluster analyses all favor significantly higher matter densities suggests the presence of systematic errors in the data or an incomplete modeling of the relevant physics. Cross checks with X-ray and microwave data, as well as independent constraints on the observable--mass relation from SZ selected clusters, suggest that the discrepancy resides in our modeling of the weak lensing signal rather than the cluster abundance. Repeating our analysis using a higher richness threshold ($\lambda \ge 30$) significantly reduces the tension with other probes, and points to one or more richness-dependent effects not captured by our model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize

Interactions between MADS-box transcription factors are critical in the regulation of floral development, and shifting MADS-box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS-box protein function remains unknown. To assess the impact of changing MADS-box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS-box proteins vary. We tested the functional consequences of this evolutionary variability using maize as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to downstream gene expression. Differential dimerization also affected B-class complex composition and abundance, independent of transcript levels. This indicates that differential B-class dimerization affects protein degradation, revealing an important consequence for evolutionary variability in MADS-box interactions. Our results highlight complexity in the evolution of developmental gene networks - changing protein-protein interactions could affect not only the composition of transcription factor complexes, but also their degradation and persistence in developing flowers. Here, our results also show how coding change in a pleiotropic master regulator could have small, quantitative effects on development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression

The shifts in adaptive strategies revealed by ecological succession and the mechanisms that facilitate these shifts are fundamental to ecology. These adaptive strategies could be particularly important in communities of arbuscular mycorrhizal fungi (AMF) mutualistic with sorghum, where strong AMF succession replaces initially ruderal species with competitive ones and where the strongest plant response to drought is to manage these AMF. Although most studies of agriculturally important fungi focus on parasites, the mutualistic symbionts, AMF, constitute a research system of human-associated fungi whose relative simplicity and synchrony are conducive to experimental ecology. First, we hypothesize that, when irrigation is stopped to mimic drought, competitive AMF species should be replaced by AMF species tolerant to drought stress. We then, for the first time, correlate AMF abundance and host plant transcription to test two novel hypotheses about the mechanisms behind the shift from ruderal to competitive AMF. Surprisingly, despite imposing drought stress, we found no stress-tolerant AMF, probably due to our agricultural system having been irrigated for nearly six decades. Remarkably, we found strong and differential correlation between the successional shift from ruderal to competitive AMF and sorghum genes whose products (i) produce and release strigolactone signals, (ii) perceive mycorrhizal-lipochitinoligosaccharide (Myc-LCO) signals, (iii) provide plant lipid and sugar to AMF, and (iv) import minerals and water provided by AMF. These novel insights frame new hypotheses about AMF adaptive evolution and suggest a rationale for selecting AMF to reduce inputs and maximize yields in commercial agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts

Abstract Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial‐microbial holobiont (termed HT‐58‐2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a , complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH 2 Cl 2 /2‐propanol, 1:1) of HT‐58‐2 cultures with NaBH 4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17‐dioxobacteriochlorins) exhibit a bathochromic shift ( λ abs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 13 1 ‐oxochlorin) exhibits a hypsochromic shift ( λ abs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λ em 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non‐axenic cultures at microscale quantities (2 mL, 2 μ m ), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT‐58‐2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.

Nguyen, Kathy‐Uyen↗
DOE OSTI2020

An algal enzyme required for biosynthesis of the most abundant marine carotenoids

Fucoxanthin and its derivatives are the main light-harvesting pigments in the photosynthetic apparatus of many chromalveolate algae and represent the most abundant carotenoids in the world’s oceans, thus being major facilitators of marine primary production. A central step in fucoxanthin biosynthesis that has been elusive so far is the conversion of violaxanthin to neoxanthin. Here, we show that in chromalveolates, this reaction is catalyzed by violaxanthin de-epoxidase–like (VDL) proteins and that VDL is also involved in the formation of other light-harvesting carotenoids such as peridinin or vaucheriaxanthin. VDL is closely related to the photoprotective enzyme violaxanthin de-epoxidase that operates in plants and most algae, revealing that in major phyla of marine algae, an ancient gene duplication triggered the evolution of carotenoid functions beyond photoprotection toward light harvesting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Arbuscular Mycorrhizal Tree Communities Have Greater Soil Fungal Diversity and Relative Abundances of Saprotrophs and Pathogens than Ectomycorrhizal Tree Communities

Trees associating with different mycorrhizas often differ in their effects on litter decomposition, nutrient cycling, soil organic matter (SOM) dynamics, and plant-soil interactions. For example, due to differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree leaf and root traits, ECM-associated soil has lower rates of C and N cycling and lower N availability than AM-associated soil. These observations suggest that many groups of nonmycorrhizal fungi should be affected by the mycorrhizal associations of dominant trees through controls on nutrient availability. To test this overarching hypothesis, we explored the influence of predominant forest mycorrhizal type and mineral N availability on soil fungal communities using next-generation amplicon sequencing. Soils from four temperate hardwood forests in southern Indiana, United States, were studied; three forests formed a natural gradient of mycorrhizal dominance (100% AM tree basal area to 100% ECM basal area), while the fourth forest contained a factorial experiment testing long-term N addition in both dominant mycorrhizal types. We found that overall fungal diversity, as well as the diversity and relative abundance of plant pathogenic and saprotrophic fungi, increased with greater AM tree dominance. Additionally, tree community mycorrhizal associations explained more variation in fungal community composition than abiotic variables, including soil depth, SOM content, nitrification rate, and mineral N availability. Our findings suggest that tree mycorrhizal associations may be good predictors of the diversity, composition, and functional potential of soil fungal communities in temperate hardwood forests. These observations help explain differing biogeochemistry and community dynamics found in forest stands dominated by differing mycorrhizal types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

ABSTRACT Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions. IMPORTANCE Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metagenomes from 25 Low-Abundance Microbes in a Partial Nitritation Anammox Microbiome

Microbial communities using anammox bacteria to remove nitrogen are increasingly important in wastewater treatment. We report on 25 metagenome-assembled genomes of low-abundance microbes from a partial nitritation anammox bioreactor system that have not been described previously. These data add to the body of information about this important wastewater treatment system.

Beach, Natalie K.↗
DOE OSTI2025

RB-TnSeq barcode abundance data sets for Novosphingobium aromaticivorans grown on the β-5-linked aromatic dimer dehydrodiconiferyl alcohol

ABSTRACT A randomly barcoded transposon insertion sequencing (RB-TnSeq) library of Novosphingobium aromaticivorans DSM12444 was grown in media containing either glucose or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) as the sole carbon source. The cultures were grown to saturation and then sequenced, yielding the barcode abundance data sets presented here.

Metz, Fletcher↗