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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi

Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Soil moisture estimation using tomographic ground penetrating radar in a MCMC–Bayesian framework

In this paper, we focus on a hydrogeological inverse problem specifically targeting monitoring soil moisture variations using tomographic ground penetrating radar (GPR) travel time data. Technical challenges exist in the inversion of GPR tomographic data for handling non-uniqueness, nonlinearity and high-dimensionality of unknowns. We have developed a new method for estimating soil moisture fields from crosshole GPR data. It uses a pilot-point method to provide a low-dimensional representation of the relative dielectric permittivity field of the soil, which is the primary object of inference: the field can be converted to soil moisture using a petrophysical model. We integrate a multi-chain Markov chain Monte Carlo (MCMC)–Bayesian inversion framework with the pilot point concept, a curved-ray GPR travel time model, and a sequential Gaussian simulation algorithm, for estimating the dielectric permittivity at pilot point locations distributed within the tomogram, as well as the corresponding geostatistical parameters (i.e., spatial correlation range). We infer the dielectric permittivity as a probability density function, thus capturing the uncertainty in the inference. The multi-chain MCMC enables addressing high-dimensional inverse problems as required in the inversion setup. The method is scalable in terms of number of chains and processors, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. The proposed inversion approach can successfully approximate the posterior density distributions of the pilot points, and capture the true values. The computational efficiency, accuracy, and convergence behaviors of the inversion approach were also systematically evaluated, by comparing the inversion results obtained with different levels of noises in the observations, increased observational data, as well as increased number of pilot points.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2007

A First Approach to Global Runoff Simulation using Satellite Rainfall Estimation

Many hydrological models have been introduced in the hydrological literature to predict runoff but few of these have become common planning or decision-making tools, either because the data requirements are substantial or because the modeling processes are too complicated for operational application. On the other hand, progress in regional or global rainfall-runoff simulation has been constrained by the difficulty of measuring spatiotemporal variability of the primary causative factor, i.e. rainfall fluxes, continuously over space and time. Building on progress in remote sensing technology, researchers have improved the accuracy, coverage, and resolution of rainfall estimates by combining imagery from infrared, passive microwave, and space-borne radar sensors. Motivated by the recent increasing availability of global remote sensing data for estimating precipitation and describing land surface characteristics, this note reports a ballpark assessment of quasi-global runoff computed by incorporating satellite rainfall data and other remote sensing products in a relatively simple rainfall-runoff simulation approach: the Natural Resources Conservation Service (NRCS) runoff Curve Number (CN) method. Using an Antecedent Precipitation Index (API) as a proxy of antecedent moisture conditions, this note estimates time-varying NRCS-CN values determined by the 5-day normalized API. Driven by multi-year (1998-2006) Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis, quasi-global runoff was retrospectively simulated with the NRCS-CN method and compared to Global Runoff Data Centre data at global and catchment scales. Results demonstrated the potential for using this simple method when diagnosing runoff values from satellite rainfall for the globe and for medium to large river basins. This work was done with the simple NRCS-CN method as a first-cut approach to understanding the challenges that lie ahead in advancing the satellite-based inference of global runoff. We expect that the successes and limitations revealed in this study will lay the basis for applying more advanced methods to capture the dynamic variability of the global hydrologic process for global runoff monlto~ngin real time. The essential ingredient in this work is the use of global satellite-based rainfall estimation.

Hong, Yang↗
DOE OSTI2018

Graphite Characterization: Baseline Variability Analysis Report

The Idaho National INL’s Baseline Material Property program provides many measurements of different material properties on a variety of nuclear graphite grades being investigated for irradiation-induced changes in material properties. The baseline material properties provide an unirradiated reference for comparison with measurements of those properties after irradiation. This study describes how uncertainty, or variance, in estimates of important material properties, like compressive strength, may depend on sample size, sample distribution and parameter estimation methods. Compressive strength data from two large collections of specimens from a billet of PCEA graphite (sample size = 230) and a billet of IG-110 graphite (sample size = 48) are used to illustrate these dependencies. The grades of graphite used represent approximate end members in terms of relative variability in strength measurements. Monte Carlo simulation and bootstrapping methods were used to examine variance in Weibull-parameter estimates as a function of sample size. Results were consistent with what previous statistical analyses have shown about the relationship between sample size and width of the confidence interval for maximum likelihood (ML) estimated parameters when samples are repeatedly drawn from a Weibull distribution. As a function of sample size, the precision of the modulus estimate increases faster than that of the characteristic strength. The modulus maximum likelihood estimates (MLEs) are biased for low sample sizes. The American Society for Testing and Materials document ASTM D7846-16 provides equations that describe the dependence of the variance of parameter MLEs on sample size. Using the same methodology, we show that the polynomials provided for variance dependence on sample size are inaccurate for sample sizes greater than ~120. We provide approximations to that relationship that illustrate relative constancy for sample size > ~10, in the logspace relationship of the modulus variance and the log transformed characteristic strength variance. Bootstrapping provided a means of comparing Weibull parameters obtained using ASME’s guidance for specimen collection to those obtained using different weighting in a case where strength is related to position in a billet and to grain orientation and a single distribution is used to characterize the billet. ASME specifies that samples be collected with equal representation in all locations and grain orientations. Parameter values obtained using ASME’s method were different from those obtained using random sampling of the complete data sets, and this was particularly true for the PCEA data. In addition, while the ASME approach yielded more conservative parameters for the PCEA data, the opposite was true for the IG-110 data. The difference observed for the PCEA data set likely reflects the larger number of against-grain specimens collected, which had generally higher strength than the with-grain specimens. This emphasizes the importance of the dependence of strength on location or grain orientation and suggests that it may be prudent to weight specimen collection toward the weaker subgroups if a conservative estimate as desired, as the equal weighting method recommended by ASME would will not always provide the most conservative Weibull parameters. Because spatial correlations commonly exist in certain grades of graphite, future work may involve developing a methodology for parameter inference that relaxes the assumption of independent specimens. ASTM and ASME codes recommend different parameter estimation methods and models of the Weibull distribution in different situations. Descriptions of the effects on parameter estimates for the example billets used in this study provide an example of how the method may affect the parameter estimate, and how—in this case—that compares to differences due to other factors, such as sample size and dependence on grain orientation or sample location.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Deriving spatially explicit direct and indirect interaction networks from animal movement data

Abstract Quantifying spatiotemporally explicit interactions within animal populations facilitates the understanding of social structure and its relationship with ecological processes. Data from animal tracking technologies (Global Positioning Systems [“GPS”]) can circumvent longstanding challenges in the estimation of spatiotemporally explicit interactions, but the discrete nature and coarse temporal resolution of data mean that ephemeral interactions that occur between consecutive GPS locations go undetected. Here, we developed a method to quantify individual and spatial patterns of interaction using continuous‐time movement models (CTMMs) fit to GPS tracking data. We first applied CTMMs to infer the full movement trajectories at an arbitrarily fine temporal scale before estimating interactions, thus allowing inference of interactions occurring between observed GPS locations. Our framework then infers indirect interactions—individuals occurring at the same location, but at different times—while allowing the identification of indirect interactions to vary with ecological context based on CTMM outputs. We assessed the performance of our new method using simulations and illustrated its implementation by deriving disease‐relevant interaction networks for two behaviorally differentiated species, wild pigs ( Sus scrofa ) that can host African Swine Fever and mule deer ( Odocoileus hemionus ) that can host chronic wasting disease. Simulations showed that interactions derived from observed GPS data can be substantially underestimated when temporal resolution of movement data exceeds 30‐min intervals. Empirical application suggested that underestimation occurred in both interaction rates and their spatial distributions. CTMM‐Interaction method, which can introduce uncertainties, recovered majority of true interactions. Our method leverages advances in movement ecology to quantify fine‐scale spatiotemporal interactions between individuals from lower temporal resolution GPS data. It can be leveraged to infer dynamic social networks, transmission potential in disease systems, consumer–resource interactions, information sharing, and beyond. The method also sets the stage for future predictive models linking observed spatiotemporal interaction patterns to environmental drivers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Inference of molecular divertor density from filtered camera analysis of molecularly induced Balmer line emission during detachment in JET L-mode plasmas

Here a previously presented Monte Carlo method for estimating local plasma conditions in 2D based on intensity ratios of deuterium Balmer D α , D γ and D ε lines was amended to consider also the D α and D γ emission contributions arising from molecular processes. The obtained estimates were used to infer the molecular divertor density with the help of the molecular databases of EIRENE. The method was benchmarked against EDGE2D-EIRENE simulations and observed to reproduce the molecularly induced emission fractions and the molecular divertor densities primarily within 25% of the references. Experimental analysis of a JET L-mode density scan suggested molecularly induced D α and D γ contributions of up to 60–70% and 20%, respectively, during the process of detachment. The independent estimates of the molecular divertor density inferred from the obtained molecularly induced D α and D γ intensities agree within uncertainties with each other. Both estimates show the molecular density increasing up to approximately 1.0–2.0 x 10 20 m -3 at the outer strike point in deep detachment with its ratio to the local electron density agreeing with EDGE2D-EIRENE predictions within the scatter of the experimental data.

interferometry↗
NASA NTRS1988

Volcanic ash layers in blue ice fields (Beardmore Glacier Area, Antarctica): Iridium enrichments

Dust bands on blue ice fields in Antarctica have been studied and have been identified to originate from two main sources: bedrock debris scraped up from the ground by the glacial movement (these bands are found predominantly at fractures and shear zones in the ice near moraines), and volcanic debris deposited on and incorporated in the ice by large-scale eruptions of Antarctic (or sub-Antractic) volcanoes. Ice core studies have revealed that most of the dust layers in the ice cores are volcanic (tephra) deposits which may be related to some specific volcanic eruptions. These eruptions have to be related to some specific volcanic eruptions. These eruptions have to be relatively recent (a few thousand years old) since ice cores usually incorporate younger ice. In contrast, dust bands on bare blue ice fields are much older, up to a few hundred thousand years, which may be inferred from the rather high terrestrial age of meteorites found on the ice and from dating the ice using the uranium series method. Also for the volcanic ash layers found on blue ice fields correlations between some specific volcanoes (late Cenozoic) and the volcanic debris have been inferred, mainly using chemical arguments. During a recent field expedition samples of several dust bands found on blue ice fields at the Lewis Cliff Ice Tongue were taken. These dust band samples were divided for age determination using the uranium series method, and chemical investigations to determine the source and origin of the dust bands. The investigations have shown that most of the dust bands found at the Ice Tongue are of volcanic origin and, for chemical and petrological reasons, may be correlated with Cenozoic volcanoes in the Melbourne volcanic province, Northern Victoria Land, which is at least 1500 km away. Major and trace element data have been obtained and have been used for identification and correlation purposes. Recently, some additional trace elements were determined in some of the dust band samples, including Ir. Iridium determinations were made using INAA, with synthetical and natural (meteorite) standards. These findings are discussed.

Koeberl, Christian↗
DOE OSTI2024

Applications of emulation and Bayesian methods in heavy-ion physics

Abstract Heavy-ion collisions provide a window into the properties of many-body systems of deconfined quarks and gluons. Understanding the collective properties of quarks and gluons is possible by comparing models of heavy-ion collisions to measurements of the distribution of particles produced at the end of the collisions. These model-to-data comparisons are extremely challenging, however, because of the complexity of the models, the large amount of experimental data, and their uncertainties. Bayesian inference provides a rigorous statistical framework to constrain the properties of nuclear matter by systematically comparing models and measurements. This review covers model emulation and Bayesian methods as applied to model-to-data comparisons in heavy-ion collisions. Replacing the model outputs (observables) with Gaussian process emulators is key to the Bayesian approach currently used in the field, and both current uses of emulators and related recent developments are reviewed. The general principles of Bayesian inference are then discussed along with other Bayesian methods, followed by a systematic comparison of seven recent Bayesian analyses that studied quark-gluon plasma properties, such as the shear and bulk viscosities. The latter comparison is used to illustrate sources of differences in analyses, and what it can teach us for future studies.

Paquet, Jean-François (ORCID:0000000187368171)↗
DOE OSTI2022

Using discrete Bayesian networks for diagnosing and isolating cross-level faults in HVAC systems

Fault detection and diagnosis (FDD) technologies are critical to ensure satisfactory building performance, such as reducing energy wastes and negative impacts on occupant comfort and productivity. Existing FDD technologies mainly focus on component-level FDD solutions, which could lead to mis-diagnosis of cross-level faults in heating, ventilating, and air-conditioning (HVAC) systems. Cross-level faults are those faults that occur in one component or subsystem, but cause operational abnormalities in other components or subsystems, and result in a building level performance degradation. How to effectively diagnose the root cause of a cross-level fault is the focus of this study. Here, this paper presents a novel discrete Bayesian Network (DisBN)-based method for diagnosing cross-level faults in an HVAC system commonly used in commercial buildings. A two-level DisBN structure model is developed in this study. The parameters used in the DisBN model are obtained either from expert knowledge or through machine-learning strategies from normal system operation data. Meanwhile, the probability parameters are discretized to incorporate the uncertainties associated with typical expert knowledge. Thus, the developed DisBN method addresses the challenges many other BN based FDD methods face, i.e., the lack of fault data for BN parameter training. The developed DisBN represents causal relationships between a fault and its cross-level system impacts (i.e., fault symptoms or fault indicators) by considering how fault impacts propagate across different levels in an HVAC system. A weather and schedule information-based Pattern Matching (WPM) method is employed to automatically create WPM baseline data sets for each incoming real time snapshot data from the building systems. Consequently, BN inference and real-time diagnostics are achieved by comparing incoming snapshot data and the WPM baseline data set. The proposed method is evaluated using experimental fault data collected in a campus building. Fault diagnosis results demonstrate that the WPM-DisBN method is effective at locating the root causes of cross-level faults in an HVAC system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Al2O3 Atomic Layer Deposition on Nanostructured γ-Mg(BH4)2 for H2 Storage

In the context of the growing hydrogen (H 2 ) economy, the demand for H 2 storage materials is high, and metal borohydrides are of particular interest. Magnesium borohydride, Mg(BH 4 ) 2 , has one of the highest hydrogen capacities of all known metal hydrides (14.9 wt % H) but suffers from high operating temperatures, slow kinetics for (de)hydrogenation, and the loss of capacity upon cycling. Strategies to address these challenges include nanoencapsulation and the use of chemical additives. This work is the first to utilize these two strategies simultaneously by using atomic layer deposition (ALD). For this new approach to modify borohydrides, we chose the well-studied Al 2 O 3 ALD process using trimethylaluminum and water. Although there has been limited use of aluminum-based additives for Mg(BH 4 ) 2 , we demonstrate that the low-temperature H 2 capacity was doubled, desorption kinetics were increased by a factor of 3, and 100 cycles of Al 2 O 3 suppressed the release of diborane compared to the uncoated Mg(BH4)2. We identified that the use of trimethylaluminum and water in the ALD process affected the decomposition pathway and that the Al 2 O 3 film growth is dominated by infiltration due to the high porosity of the ..gamma..-phase Mg(BH 4 ) 2 . From these results, the potential of ALD as a method to functionalize solid-state H 2 storage materials is inferred, and recommendations for future ALD processes are presented.

08 HYDROGEN↗
DOE OSTI2025

The Nature of Standing Plasma Waves Following Fast Breakdown in Thunderstorms

Narrow bipolar events (NBEs) are produced by large-scale systems of streamer corona discharges that occur inside thunderstorms and radiate intensely at very-high frequencies. Here we examine 14 high-power NBEs recorded in Florida which are followed by a lasting oscillatory signal. We isolate the dominant frequencies of the oscillations using empirical mode decomposition methods, and cross-reference this information with the radiator size inferred from broadband interferometry. We conclude that the oscillations are evidence of a standing electromagnetic wave in the plasma cavity created by the preceding streamer system, that is, the cavity's fundamental mode with wavelength equal to twice the radiator length. Contrasting the dispersive and attenuation properties of these waves across several different events allows us to conclude that the cavity is filled with ions resulting in an average conductivity of 0.01–0.1 mS/m, which are left behind after the streamers decay via electron attachment to oxygen molecules.

58 GEOSCIENCES↗
DOE OSTI2017

A model independent safeguard against background mismodeling for statistical inference

We propose a safeguard procedure for statistical inference that provides universal protection against mismodeling of the background. The method quantifies and incorporates the signal-like residuals of the background model into the likelihood function, using information available in a calibration dataset. This prevents possible false discovery claims that may arise through unknown mismodeling, and corrects the bias in limit setting created by overestimated or underestimated background. We demonstrate how the method removes the bias created by an incomplete background model using three realistic case studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Early retirement of power plants in climate mitigation scenarios

International efforts to avoid dangerous climate change aim for large and rapid reductions of fossil fuel CO 2 emissions worldwide, including nearly complete decarbonization of the electric power sector. However, achieving such rapid reductions may depend on early retirement of coal- and natural gas-fired power plants. Here, we analyze future fossil fuel electricity demand in 171 energy-emissions scenarios from Integrated Assessment Models (IAMs), evaluating the implicit retirements and/or reduced operation of generating infrastructure. Although IAMs calculate retirements endogenously, the structure and methods of each model differ; we use a standard approach to infer retirements in outputs from all six major IAMs and—unlike the IAMs themselves—we begin with the age distribution and region-specific operating capacities of the existing power fleet. We find that coal-fired power plants in scenarios consistent with international climate targets (i.e. keeping global warming well-below 2 °C or 1.5 °C) retire one to three decades earlier than historically has been the case. If plants are built to meet projected fossil electricity demand and instead allowed to operate at the level and over the lifetimes they have historically, the roughly 200 Gt CO 2 of additional emissions this century would be incompatible with keeping global warming well-below 2 °C. Thus, ambitious climate mitigation scenarios entail drastic, and perhaps un-appreciated, changes in the operating and/or retirement schedules of power infrastructure.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2021

Dark matter haloes of massive elliptical galaxies at z ∼ 0.2 are well described by the Navarro–Frenk–White profile

ABSTRACT We investigate the internal structure of elliptical galaxies at z ∼ 0.2 from a joint lensing–dynamics analysis. We model Hubble Space Telescope images of a sample of 23 galaxy–galaxy lenses selected from the Sloan Lens ACS (SLACS) survey. Whereas the original SLACS analysis estimated the logarithmic slopes by combining the kinematics with the imaging data, we estimate the logarithmic slopes only from the imaging data. We find that the distribution of the lensing-only logarithmic slopes has a median 2.08c ± 0.03 and intrinsic scatter 0.13 ± 0.02, consistent with the original SLACS analysis. We combine the lensing constraints with the stellar kinematics and weak lensing measurements, and constrain the amount of adiabatic contraction in the dark matter (DM) haloes. We find that the DM haloes are well described by a standard Navarro–Frenk–White halo with no contraction on average for both of a constant stellar mass-to-light ratio (M/L) model and a stellar M/L gradient model. For the M/L gradient model, we find that most galaxies are consistent with no M/L gradient. Comparison of our inferred stellar masses with those obtained from the stellar population synthesis method supports a heavy initial mass function (IMF) such as the Salpeter IMF. We discuss our results in the context of previous observations and simulations, and argue that our result is consistent with a scenario in which active galactic nucleus feedback counteracts the baryonic-cooling-driven contraction in the DM haloes.

Shajib, Anowar J.↗
DOE OSTI2017

Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment. Workshop report, September 21–23, 2016

The Biological Systems Science Division (BSSD) within the U.S. Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) funds basic research on plants and microbes relevant to several DOE bioenergy and environmental mission areas. BSSD’s long history of developing and supporting genomic characterization of biological systems has led, in part, to the high-throughput DNA sequencing technology available to researchers worldwide. In recent years, genome sequencing has vastly outpaced the ability to interpret genome function. Fully maximizing this wealth of data will require new technology advancements, along with improvements and an increase in the throughput of existing methods for characterizing molecular- to cellular-level processes important for inferring biological function. BSSD research seeks to understand the fundamental genome-encoded properties of plants and microbes that can be harnessed or redesigned for beneficial purposes. Current emphases are leading to the discovery, development, and understanding of numerous plant and microbial species with traits suitable for the production of fuels and chemical products from renewable biomass that could be grown synergistically with food or animal feed crops while not competing with other societal needs. Additionally, BSSD further supports research leading to an understanding of the complex and essential interactions among plants, microbial communities, and the environment to find new ways to sustainably produce biomass for a range of bioenergy and bioproduct applications. This research also is relevant for incorporation into larger-scale environmental models such as those developed through the research supported by BER’s Earth and Environmental Systems Sciences programs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Constructing Regulatory Networks to Compare Axenic and Interspecies Microbial Gene Transcription

In this preliminary study, we constructed gene regulatory networks (GRNs) from transcriptional expression data of axenic and interspecies microbial cultures with the goal of predicting how cocultivation affected greenhouse gas respiration by these species. The specific strains of Methylotuvimicrobium alkaliphilum 20Z, a methylotroph, and Cyanobacterium stanieri HL-69, a phototroph, were chosen for their viability in industrial bioprocessing. We ranked directed interactions between gene pairs based on the ability of the input gene to predict the expression of a target gene relative to their transcriptomes. While we were able to identify topological differences between conditions, our initial findings require validation through experimental analysis and further modeling. We aimed to develop a systematic thresholding approach to optimize the accuracy of our networks. We filtered out trial networks separately from top gene interactions of the scored rankings. Parameters of unfiltered and filtered networks were used to test and develop thresholding approaches. Knee point detection of edge weight distributions was explored as an approach for separating significant interactions from insignificant interactions in unfiltered networks. While knee detection failed to produce analogous networks for broad cross-condition comparisons, the results informed us about the proportions of significant edges present in unfiltered networks. We also calculated the average mean degree for nodes in a selection of trial networks to find a thresholding value characteristic to all groups. While we did not reach a definitive conclusion, we gained insight into the coregulatory structures of our groups and made critical evaluations of systematic methods for filtering networks. We recommend an iterative process for the inference of GRNs, where the most significant results from preliminary explorations are used to improve the efficiency with which regulatory motifs are chosen for experimental characterization. Experimental results can then inform the framework of adjusted models to improve broad interpretations of GRNs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Spectroscopic determination of masses (and implied ages) for red giants

The mass of a star is arguably its most fundamental parameter. For red giant stars, tracers luminous enough to be observed across the Galaxy, mass implies a stellar evolution age. It has proven to be extremely difficult to infer ages and masses directly from red giant spectra using existing methods. From the Kepler and apogee surveys, samples of several thousand stars exist with high-quality spectra and asteroseismic masses. Here we show that from these data we can build a data-driven spectral model using The Cannon, which can determine stellar masses to ∼0.07 dex from apogee dr12 spectra of red giants; these imply age estimates accurate to ∼0.2 dex (40%). We show that The Cannon constrains these ages foremost from spectral regions with CN absorption lines, elements whose surface abundances reflect mass-dependent dredge-up. We deliver an unprecedented catalog of 70,000 giants (including 20,000 red clump stars) with mass and age estimates, spanning the entire disk (from the Galactic center to R∼20 kpc). We show that the age information in the spectra is not simply a corollary of the birth-material abundances [Fe/H] and [α/Fe], and that, even within a monoabundance population of stars, there are age variations that vary sensibly with Galactic position. Such stellar age constraints across the Milky Way open up new avenues in Galactic archeology.

79 ASTRONOMY AND ASTROPHYSICS↗