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DOE OSTI2021

Active layer thickness as a function of soil water content

Active layer thickness (ALT) is a critical metric for monitoring permafrost. How soil moisture influences ALT depends on two competing hypotheses: (a) increased soil moisture increases the latent heat of fusion for thaw, resulting in shallower active layers, and (b) increased soil moisture increases soil thermal conductivity, resulting in deeper active layers. To investigate their relative influence on thaw depth, we analyzed the Field Measurements of Soil Moisture and Active Layer Thickness (SMALT) in Alaska and Canada dataset, consisting of thousands of measurements of thaw depth and soil moisture collected at dozens of sites across Alaska and Canada as part of NASA’s Arctic Boreal Vulnerability Experiment (ABoVE). As bulk volumetric water content (VWC) integrated over the entire active layer increases, ALT decreases, supporting the latent heat hypothesis. However, as VWC in the top 12 cm of soil increases, ALT increases, supporting the thermal conductivity hypothesis. Regional temperature variations determine the baseline thaw depth while precipitation may influence the sensitivity of ALT to changes in VWC. Soil latent heat dominates over thermal conductivity in determining ALT, and the effect of bulk VWC on ALT appears consistent across sites.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2012

BARYON CONTENT OF MASSIVE GALAXY CLUSTERS AT z = 0-0.6

We study the relationship between two major baryonic components in galaxy clusters, namely the stars in galaxies and the ionized gas in the intracluster medium (ICM), using 94 clusters that span the redshift range 0-0.6. Accurately measured total and ICM masses from Chandra observations and stellar masses derived from the Wide-field Infrared Survey Explorer and the Two Micron All Sky Survey allow us to trace the evolution of cluster baryon content in a self-consistent fashion. We find that, within r{sub 500}, the evolution of the ICM-mass-total-mass relation is consistent with the expectation of the self-similar model, while there is no evidence for redshift evolution in the stellar-mass-total-mass relation. This suggests that the stellar mass and ICM mass in the inner parts of clusters evolve differently.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2013

THE LYMAN ALPHA REFERENCE SAMPLE: EXTENDED LYMAN ALPHA HALOS PRODUCED AT LOW DUST CONTENT

We report on new imaging observations of the Lyman alpha emission line (Ly{alpha}), performed with the Hubble Space Telescope, that comprise the backbone of the Lyman alpha Reference Sample. We present images of 14 starburst galaxies at redshifts 0.028 < z < 0.18 in continuum-subtracted Ly{alpha}, H{alpha}, and the far ultraviolet continuum. We show that Ly{alpha} is emitted on scales that systematically exceed those of the massive stellar population and recombination nebulae: as measured by the Petrosian 20% radius, R{sub P20}, Ly{alpha} radii are larger than those of H{alpha} by factors ranging from 1 to 3.6, with an average of 2.4. The average ratio of Ly{alpha}-to-FUV radii is 2.9. This suggests that much of the Ly{alpha} light is pushed to large radii by resonance scattering. Defining the Relative Petrosian Extension of Ly{alpha} compared to H{alpha}, {xi}{sub Ly{alpha}} = R {sup Ly{alpha}}{sub P20}/R {sup H{alpha}}{sub P20}, we find {xi}{sub Ly{alpha}} to be uncorrelated with total Ly{alpha} luminosity. However, {xi}{sub Ly{alpha}} is strongly correlated with quantities that scale with dust content, in the sense that a low dust abundance is a necessary requirement (although not the only one) in order to spread Ly{alpha} photons throughout the interstellar medium and drive a large extended Ly{alpha} halo.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability and implementation All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary data are available at Bioinformatics online.

Hagemeijer, Marne C.↗

DOE OSTI2021

Information content of higher order galaxy correlation functions

The shapes of galaxy N-point correlation functions can be used as standard rulers to constrain the distance–redshift relationship. The cosmological density fields traced by late-time galaxy formation are initially nearly Gaussian, and hence, all the cosmological information can be extracted from their two-point correlation function. Subsequent non-linear evolution under gravity, as well as halo and then galaxy formation, generates higher order correlation functions. Since the mapping of the initial to the final density field is, on large scales, invertible, it is often claimed that the information content of the initial field’s power spectrum is equal to that of all the higher order functions of the final, non-linear field. This claim implies that reconstruction of the initial density field from the non-linear field renders analysis of higher order correlation functions of the latter superfluous. We show that this claim is false when the N-point functions are used as standard rulers. Constraints available from joint analysis of the two and three-point correlation functions can, in some cases, exceed those offered by the initial power spectrum. We provide a mathematical justification for this claim and demonstrate it using a large suite of N-body simulations. In particular, we show that for the z = 0 real-space matter field in the limit of vanishing shot-noise, taking modes up to k max = 0.2 h Mpc −1 , using the bispectrum alone offers a factor of 2 reduction in the variance on the cosmic distance scale relative to that available from the linear power spectrum.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

MASCOT: an ESO–ARO legacy survey of molecular gas in nearby SDSS-MaNGA galaxies - I. First data release, and global and resolved relations between H 2 and stellar content

We present the first data release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA)–Arizona Radio Observatory (ARO) Survey of CO Targets (MASCOT), a European Southern Observatory public spectroscopic survey conducted at the ARO. We measure the CO(1–0) line emission in a sample of 187 nearby galaxies selected from the MaNGA survey that has obtained integral field unit (IFU) spectroscopy for a sample of ~10 000 galaxies at low redshift. The main goal of MASCOT is to probe the molecular gas content of star-forming galaxies with stellar masses >10 9.5 M ⊙ and with associated MaNGA IFU observations and well-constrained quantities like stellar masses, star formation rates, and metallicities. In this paper, we present the first results of the MASCOT survey, providing integrated CO(1–0) measurements that cover several effective radii of the galaxy and present CO luminosities, CO kinematics, and estimated H 2 gas masses. We observe that the decline of the galaxy star formation rate with respect to the star formation main sequence increases with the decrease of molecular gas and with a reduced star formation efficiency, in agreement with results of other integrated studies. Relating the molecular gas mass fractions with the slope of the stellar age gradients inferred from the MaNGA observations, we find that galaxies with lower molecular gas mass fractions tend to show older stellar populations close to the galactic centre, while the opposite is true for galaxies with higher molecular gas mass fractions, providing tentative evidence for inside-out quenching.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

H i content of massive red spiral galaxies observed by FAST

ABSTRACT A sample of 279 massive red spirals was selected optically by Guo et al., among which 166 galaxies have been observed by the ALFALFA survey. In this work, we observe H i content of the rest 113 massive red spiral galaxies using the Five-hundred-meter Aperture Spherical radio Telescope (FAST). 75 of the 113 galaxies have H i detection with a signal-to-noise ratio (S/N) greater than 4.7. Compared with the red spirals in the same sample that have been observed by the ALFALFA survey, galaxies observed by FAST have on average a higher S/N, and reach to a lower H i mass. To investigate why many red spirals contain a significant amount of H i mass, we check colour profiles of the massive red spirals using images observed by the DESI Legacy Imaging Surveys. We find that galaxies with H i detection have bluer outer discs than the galaxies without H i detection, for both ALFALFA and FAST samples. For galaxies with H i detection, there exists a clear correlation between galaxy H i mass and g-r colour at outer radius: galaxies with higher H i masses have bluer outer discs. The results indicate that optically selected massive red spirals are not fully quenched, and the H i gas observed in many of the galaxies may exist in their outer blue discs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

The H I content of red geyser galaxies

Red geysers are a specific type of quiescent galaxy, denoted by twin jets emerging from their galactic centres. These bisymmetric jets possibly inject energy and heat into the surrounding material, effectively suppressing star formation by stabilizing cool gas. In order to confirm the presence and evolutionary consequences of these jets, this paper discusses the scaling, stacking, and conversion of 21-cm H I flux data sourced from the H I -MaNGA survey into H I gas-to-stellar mass (G/S) spectra. Our samples were dominated by non-detections, or galaxies with weak H I signals, and consequently by H I upper limits. The stacking technique discussed successfully resolved emission features in both the red geyser G/S spectrum and the control sample G/S spectrum. From these stacked spectra, we find that on average, red geyser galaxies have G/S of 0.086 ± 0.011 (random) + 0.029 (systematic), while non-red geyser galaxies of similar stellar mass have a G/S ratio of 0.039 ± 0.018 (random) + 0.013 (systematic). Therefore, we find no statistically significant evidence that the H I content of red geysers is different from the general quiescent population.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

The bar rotation rate as a diagnostic of dark matter content in the centre of disc galaxies

We investigate the link between the bar rotation rate and dark matter content in barred galaxies by concentrating on the cases of the lenticular galaxies NGC 4264 and NGC 4277. These two gas-poor galaxies have similar morphologies, sizes, and luminosities. But, NGC 4264 hosts a fast bar, which extends to nearly the corotation, while the bar embedded in NGC 4277 is slow and falls short of corotation. We derive the fraction of dark matter ƒ DM, bar within the bar region from Jeans axisymmetric dynamical models by matching the stellar kinematics obtained with the MUSE integral-field spectrograph and using SDSS images to recover the stellar mass distribution. We build mass-follows-light models as well as mass models with a spherical halo of dark matter, which is not tied to the stars. We find that the inner regions of NGC 4277 host a larger fraction of dark matter (⁠ƒ DM,bar = 0.53±0.02⁠) with respect to NGC 4264 (⁠(⁠ƒ DM,bar = 0.33±0.04⁠) in agreement with the predictions of theoretical works and the findings of numerical simulations, which have found that fast bars live in baryon-dominated discs, whereas slow bars experienced a strong drag from the dynamical friction due to a dense DM halo. This is the first time that the bar rotation rate is coupled to fDM, bar derived from dynamical modelling.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts

Xylose is the second most abundant monomeric sugar in plant biomass. Consequently, xylose catabolism is an ecologically important trait for saprotrophic organisms, as well as a fundamentally important trait for industries that hope to convert plant mass to renewable fuels and other bioproducts using microbial metabolism. Although common across fungi, xylose catabolism is rare within Saccharomycotina, the subphylum that contains most industrially relevant fermentative yeast species. The genomes of several yeasts unable to consume xylose have been previously reported to contain the full set of genes in the XYL pathway, suggesting the absence of a gene–trait correlation for xylose metabolism. Here, we measured growth on xylose and systematically identified XYL pathway orthologs across the genomes of 332 budding yeast species. Although the XYL pathway coevolved with xylose metabolism, we found that pathway presence only predicted xylose catabolism about half of the time, demonstrating that a complete XYL pathway is necessary, but not sufficient, for xylose catabolism. We also found that XYL1 copy number was positively correlated, after phylogenetic correction, with xylose utilization. We then quantified codon usage bias of XYL genes and found that XYL3 codon optimization was significantly higher, after phylogenetic correction, in species able to consume xylose. Finally, we showed that codon optimization of XYL2 was positively correlated, after phylogenetic correction, with growth rates in xylose medium. We conclude that gene content alone is a weak predictor of xylose metabolism and that using codon optimization enhances the prediction of xylose metabolism from yeast genome sequence data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

The use of synchrotron X-ray fluorescent imaging to study distribution and content of elements in chemically fixed single cells: a case study using mouse pancreatic beta-cells

Synchrotron X-ray fluorescence microscopy (SXRF) presents a valuable opportunity to study the metallome of single cells because it simultaneously provides high-resolution subcellular distribution and quantitative cellular content of multiple elements. Different sample preparation techniques have been used to preserve cells for observations with SXRF, with a goal to maintain fidelity of the cellular metallome. In this case study, mouse pancreatic beta-cells have been preserved with optimized chemical fixation. We show that cell-to-cell variability is normal in the metallome of beta-cells due to heterogeneity and should be considered when interpreting SXRF data. Additionally, we determined the impact of several immunofluorescence (IF) protocols on metal distribution and quantification in chemically fixed beta-cells and found that the metallome of beta-cells was not well preserved for quantitative analysis. However, zinc and iron qualitative analysis could be performed after IF with certain limitations. To help minimize metal loss using samples that require IF, we describe a novel IF protocol that can be used with chemically fixed cells after the completion of SXRF.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The IMG/M data management and analysis system v.7: content updates and new features

The Integrated Microbial Genomes & Microbiomes system at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. Here, we also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Declining carbohydrate content of Sitka-spruce treesdying from seawater exposure

Abstract Increasing sea levels associated with climate change threaten the survival of coastal forests, yet the mechanisms by which seawater exposure causes tree death remain poorly understood. Despite the potentially crucial role of nonstructural carbohydrate (NSC) reserves in tree survival, their dynamics in the process of death under seawater exposure are unknown. Here we monitored progressive tree mortality and associated NSC storage in Sitka-spruce (Picea sitchensis) trees dying under ecosystem-scale increases in seawater exposure in western Washington, USA. All trees exposed to seawater, because of monthly tidal intrusion, experienced declining crown foliage during the sampling period, and individuals with a lower percentage of live foliated crown (PLFC) died faster. Tree PLFC was strongly correlated with subsurface salinity and needle ion contents. Total NSC concentrations in trees declined remarkably with crown decline, and reached extremely low levels at tree death (2.4% and 1.6% in leaves and branches, respectively, and 0.4% in stems and roots). Starch in all tissues was almost completely consumed, while sugars remained at a homeostatic level in foliage. The decreasing NSC with closer proximity to death and near zero starch at death are evidences that carbon starvation occurred during Sitka-spruce mortality during seawater exposure. Our results highlight the importance of carbon storage as an indicator of tree mortality risks under seawater exposure.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Dislocation content of grain boundary phase junctions and its relation to grain boundary excess properties

In this work, we analyze the dislocation content of grain boundary (GB) phase junctions, i.e., line defects separating two different GB phases coexisting on the same GB plane. While regular GB disconnections have been characterized for a variety of interfaces, GB phase junctions formed by GBs with different structures and different numbers of excess atoms have not been previously studied. We apply a general Burgers circuit analysis to calculate the Burgers vectors b of junctions in two Σ5 Cu boundaries previously simulated with molecular dynamics. The Burgers vectors of these junctions cannot be described by the displacement shift complete (DSC) lattice alone. We show that, in general, the normal component of b is not equal to the difference in the GB excess volumes but contains another contribution from the numbers of GB atoms per unit area ΔN* required to transform one GB phase into another. In the boundaries studied, the latter component dominates and even changes the sign of b. We derive expressions for the normal and tangential components of b in terms of the DSC lattice vectors and the non-DSC part due to ΔN* and additional GB excess properties, including excess volume and shears. These expressions provide a connection between GB phase transformations driven by the GB free energy difference and the motion of GB junctions under applied normal and shear stresses. The proposed analysis quantifies b and therefore makes it possible to calculate the elastic part of the energy of these defects, evaluate their contribution to the nucleation barrier during GB phase transformations, and treat elastic interactions with other defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Search for photons above 10 18 eV by simultaneously measuring the atmospheric depth and the muon content of air showers at the Pierre Auger Observatory

The Pierre Auger Observatory is the most sensitive instrument to detect photons with energies above 1 0 17 eV . It measures extensive air showers generated by ultrahigh energy cosmic rays using a hybrid technique that exploits the combination of a fluorescence detector with a ground array of particle detectors. The signatures of a photon-induced air shower are a larger atmospheric depth of the shower maximum ( X max ) and a steeper lateral distribution function, along with a lower number of muons with respect to the bulk of hadron-induced cascades. In this work, a new analysis technique in the energy interval between 1 and 30 EeV ( 1 EeV = 1 0 18 eV ) has been developed by combining the fluorescence detector-based measurement of X max with the specific features of the surface detector signal through a parameter related to the air shower muon content, derived from the universality of the air shower development. No evidence of a statistically significant signal due to photon primaries was found using data collected in about 12 years of operation. Thus, upper bounds to the integral photon flux have been set using a detailed calculation of the detector exposure, in combination with a data-driven background estimation. The derived 95% confidence level upper limits are 0.0403, 0.01113, 0.0035, 0.0023, and 0.0021 km − 2 sr − 1 yr − 1 above 1, 2, 3, 5, and 10 EeV, respectively, leading to the most stringent upper limits on the photon flux in the EeV range. Compared with past results, the upper limits were improved by about 40% for the lowest energy threshold and by a factor 3 above 3 EeV, where no candidates were found and the expected background is negligible. The presented limits can be used to probe the assumptions on chemical composition of ultrahigh energy cosmic rays and allow for the constraint of the mass and lifetime phase space of super-heavy dark matter particles. Published by the American Physical Society 2024

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Effects of Al content and annealing on the phases formation, lattice parameters, and magnetization of A l x F e 2 B 2 ( x = 1.0 , 1.1 , 1.2 ) alloys

AlFe 2 B 2 is a ferromagnet with the Curie temperature around 300 K and has the potential to be an outstanding rare-earth free candidate for magnetocaloric applications. However, samples prepared from the melt contain additional phases which affect the functional response of the AlFe 2 B 2 phase. Here, we report on the effects of Al content in samples with the initial (nominal) composition of Al x Fe 2 B 2 where x=1.0, 1.1, and 1.2 prepared by arc-melting followed by suction casting and annealing. The as-cast Al x Fe 2 B 2 alloys contain AlFe 2 B 2 as well as additional phases including the primary solidifying FeB and Al 13 Fe 4 compounds which are ferromagnetic and paramagnetic, respectively, at 300 K. The presence of these phases makes it difficult to extract the intrinsic magnetic properties of AlFe 2 B 2 phase. Annealing of Al x Fe 2 B 2 alloys at 1040°C for 3 days allows for reaction of the FeB with Al 13 Fe 4 to form the AlFe 2 B 2 phase, significantly reduces the amount of additional phases, and results in nearly pure AlFe 2 B2 phase as confirmed with XRD, magnetization, scanning electron microscopy, and electronic transport. The values of the magnetization, effective magnetic moment per Fe atom, specific heat capacity, electrical resistivity and Seebeck coefficient for the AlFe 2 B 2 compound have been established.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Silencing CHALCONE SYNTHASE in Maize Impedes the Incorporation of Tricin into Lignin and Increases Lignin Content

Lignin is a phenolic heteropolymer that is deposited in secondary-thickened cell walls, where it provides mechanical strength. A recent structural characterization of cell walls from monocot species showed that the flavone tricin is part of the native lignin polymer, where it is hypothesized to initiate lignin chains. In this study, we investigated the consequences of altered tricin levels on lignin structure and cell wall recalcitrance by phenolic profiling, nuclear magnetic resonance, and saccharification assays of the naturally silenced maize (Zea mays) C2-Idf (inhibitor diffuse) mutant, defective in the CHALCONE SYNTHASE Colorless2 (C2) gene. We show that the C2-Idf mutant produces highly reduced levels of apigenin- and tricin-related flavonoids, resulting in a strongly reduced incorporation of tricin into the lignin polymer. Moreover, the lignin was enriched in β-β and β-5 units, lending support to the contention that tricin acts to initiate lignin chains and that, in the absence of tricin, more monolignol dimerization reactions occur. In addition, the C2-Idf mutation resulted in strikingly higher Klason lignin levels in the leaves. As a consequence, the leaves of C2-Idf mutants had significantly reduced saccharification efficiencies compared with those of control plants. These findings are instructive for lignin engineering strategies to improve biomass processing and biochemical production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis

Glycosylinositol phosphorylceramides (GIPCs) are a class of glycosylated sphingolipids found in plants, fungi, and protozoa. These lipids are abundant in the plant plasma membrane, forming ~25% of total plasma membrane lipids. Little is known about the function of the glycosylated headgroup, but two recent studies have indicated that they play a key role in plant signaling and defense. Here, we show that a member of glycosyltransferase family 64, previously named ECTOPICALLY PARTING CELLS1, is likely a Golgi-localized GIPC-specific mannosyl-transferase, which we renamed GIPC MANNOSYL-TRANSFERASE1 (GMT1). Sphingolipid analysis revealed that the Arabidopsis thaliana gmt1 mutant almost completely lacks mannose-carrying GIPCs. Heterologous expression of GMT1 in Saccharomyces cerevisiae and tobacco (Nicotiana tabacum) cv Bright Yellow 2 resulted in the production of non-native mannosylated GIPCs. gmt1 displays a severe dwarfed phenotype and a constitutive hypersensitive response characterized by elevated salicylic acid and hydrogen peroxide levels, similar to that we previously reported for the Golgi-localized, GIPC-specific, GDP-Man transporter GONST1 (Mortimer et al., 2013). Unexpectedly, we show that gmt1 cell walls have a reduction in cellulose content, although other matrix polysaccharides are unchanged.

59 BASIC BIOLOGICAL SCIENCES↗