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DOE OSTI2021

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Abstract Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal–methanogen physical associations and fungal cell wall development and remodeling.

09 BIOMASS FUELS↗

DOE OSTI2024

Data for "Divergent urban land trajectories under alternative population projections within the shared socioeconomic pathways"

Datasets supporting findings and visualizations behind McManamay et al. (2024) Divergent urban land trajectories under alternative population projections within the shared socioeconomic pathways. Environmental Research Letters, DOI: 10.1088/1748-9326/ad2eec Using a spatial modeling experiment at high resolution (1-km), this study compared how two alternative US population projections, varying in the spatially explicit nature of demographic patterns and migration, affect urban land dynamics simulated by the Spatially Explicit, Long-term, Empirical City development (SELECT) model for SSP2, SSP3, and SSP5. The numerical experiment, inputs and outputs are fully described in McManamay et al. (2024). The datasets summarize SELECT model simulations within urban areas and rural areas of the conterminous United States. For code to reproduce the results, please refer to https://github.com/IMMM-SFA/mcmanamay_etal_2024_erl Please refer to the README file provided in Files for more details. Descriptions of the datasets are provided below. Dataset(s) Descriptions: Urban_Land_delta_UA_County.csv: Urban land area for original (default) population, updated population, and urban land delta (difference between the two) according to Shared Socioeconomic Pathways (SSPs) and year. Urban land is summarized for U.S. counties (FIPS code) and urban areas (GEOID) as unique areas within various counties. JO_Gao_pop_ufdelta.csv: Comparison of population differences and urban land differences between the origial (default) and updated population projections. City_Case_studies.csv: Differences in urban land areas arising from different population projections summarized for selected cities (Atlanta, Los Angeles, Houston, and New York) and their surrounding rural areas UA_county_FID.zip: Zipped folder of .tiff file depicting unique combination of urban areas and US counties used for summarizing urban land differences in urban and rural areas based on different population projections. ULD_clusters.zip: Zipped folder of .csv files depicting normalized changes in urban land delta (difference in urban land arising from population projections) and the respective Ward's hierarchical clusters, which group urban and rural areas based on similarities in temporal trends. Urban_Percent_change_2100.zip: Zipped folder of .csv files depicting percent changes in urban land area for year 2100 based on differences in the original (default) population and updated population. Each file is for SSPs and urban or rural areas.

Land↗

DOE OSTI2024

Design and modeling of indirectly driven magnetized implosions on the NIF

The use of magnetic fields to improve the performance of hohlraum-driven implosions on the National Ignition Facility (NIF) is discussed. The focus is on magnetically insulated inertial confinement fusion, where the primary field effect is to reduce electron-thermal and alpha-particle loss from the compressed hotspot (magnetic pressure is of secondary importance). We summarize the requirements to achieve this state. The design of recent NIF magnetized hohlraum experiments is presented. These are close to earlier shots in the three-shock, high-adiabat (BigFoot) campaign, subject to the constraints that magnetized NIF targets must be fielded at room-temperature, and use ≲1 MJ of laser energy to avoid the risk of optics damage from stimulated Brillouin scattering. We present results from the original magnetized hohlraum platform, as well as a later variant that gives a higher hotspot temperature. In both platforms, imposed fields (at the capsule center) of up to 28 T increase the fusion yield and hotspot temperature. Integrated radiation-magneto-hydrodynamic modeling with the Lasnex code of these shots is shown, where laser power multipliers and a saturation clamp on cross-beam energy transfer are developed to match the time of peak capsule emission and the P2 Legendre moment of the hotspot x-ray image. The resulting fusion yield and ion temperature agree decently with the measured relative effects of the field, although the absolute simulated yields are higher than the data by 2.0−2.7×. The tuned parameters and yield discrepancy are comparable for experiments with and without an imposed field, indicating the model adequately captures the field effects. Self-generated and imposed fields are added sequentially to simulations of one BigFoot NIF shot to understand how they alter target dynamics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Numerical simulations of laser-driven experiments of ion acceleration in stochastic magnetic fields

We present numerical simulations used to interpret laser-driven plasma experiments at the GSI Helmholtz Centre for Heavy Ion Research. The mechanisms by which non-thermal particles are accelerated in astrophysical environments, e.g., the solar wind, supernova remnants, and gamma ray bursts, is a topic of intense study. When shocks are present, the primary acceleration mechanism is believed to be first-order Fermi, which accelerates particles as they cross a shock. Second-order Fermi acceleration can also contribute, utilizing magnetic mirrors for particle energization. Despite this mechanism being less efficient, the ubiquity of magnetized turbulence in the universe necessitates its consideration. Another acceleration mechanism is the lower-hybrid drift instability, arising from gradients of both density and magnetic field, which produce lower-hybrid waves with an electric field that energizes particles as they cross these waves. With the combination of high-powered laser systems and particle accelerators, it is possible to study the mechanisms behind cosmic-ray acceleration in the laboratory. In this work, we combine experimental results and high-fidelity three-dimensional simulations to estimate the efficiency of ion acceleration in a weakly magnetized interaction region. We validate the FLASH magneto-hydrodynamic code with experimental results and use OSIRIS particle-in-cell code to verify the initial formation of the interaction region, showing good agreement between codes and experimental results. We find that the plasma conditions in the experiment are conducive to the lower-hybrid drift instability, yielding an increase in energy ΔE of ~ 264 keV for 242 MeV calcium ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Capture and migration of Jupiter and Saturn in mean motion resonance in a gaseous protoplanetary disc

Here, we study the dynamical evolution of Jupiter and Saturn embedded in a gaseous, solar nebula-type disc by means of hydrodynamics simulations with the FARGO2D1D code. We study the evolution for different initial separations of the planets’ orbits, Δa SJ , to investigate whether they become captured in mean motion resonance (MMR) and the direction of the subsequent migration of the planet (inwards or outwards). We also provide an assessment of the planet’s orbital dynamics at different epochs of Saturn’s growth. We find that the evolution of initially compact orbital configurations is dependent on the value of Δa SJ . This implies that an evolution as that proposed in the Grand Tack model depends on the precise initial orbits of Jupiter and Saturn and on the time-scales for their formation. Capture in the 1:2 MMR and inward or (nearly) stalled migration are highly favoured. Within its limits, our work suggests that the reversed migration, associated with the resonance capture of Jupiter and Saturn, may be a low-probability evolutionary scenario, so that other planetary systems with giant planets are not expected to have experienced a Grand Tack-like evolutionary path.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

The SAS4A/SASSYS-1 Version 5.8 Safety Analysis Code System

SAS4A/SASSYS-1 is a software simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced nuclear reactors. Detailed, mechanistic models of steady-state and transient thermal, hydraulic, kinetic, and mechanical phenomena are employed to describe the response of the reactor core, the reactor primary and secondary coolant loops, the reactor control and protection systems, and the balance-of-plant to accidents caused by changes in coolant flow, loss of heat rejection, or reactivity insertion. The consequences of single and double-fault accidents can be modeled, including fuel and coolant heating, fuel and cladding mechanical behavior, core reactivity feedbacks, coolant loop performance including natural circulation, and decay heat removal. Analyses are typically terminated upon demonstration of reactor and plant shutdown to permanently coolable conditions, or upon violation of design basis margins. The objective of the analysis is to quantify accident consequences as measured by the transient behavior of system performance parameters, such as fuel and cladding temperatures, reactivity, and cladding strain. Originally developed for analysis of sodium cooled reactors with oxide fuel clad by stainless steel, the models were subsequently extended and specialized to metallic fuel clad with advanced alloys and to several other coolant options, including lead, LBE, and water.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Phase contrast imaging measurements and numerical simulations of turbulent density fluctuations in gas-fuelled ECRH discharges in Wendelstein 7-X

The fundamental nature of turbulent density fluctuations in standard Wendelstein 7-X (W7-X) stellarator discharges is investigated experimentally via phase contrast imaging (PCI) in combination with gyrokinetic simulations with the code GENE. We find that density fluctuations are ion-temperature-gradient-driven and radially localised in the outer half of the plasma. It is shown that the line-integrated PCI measurements cover the right range of wavenumbers and a favourable toroidal and poloidal location to capture some of the strongest density fluctuations in W7-X. Due to the radial localisation of fluctuations, measured wavenumber–frequency spectra exhibit a dominant phase velocity, which can be related to the E × B rotation velocity at the radial position of a well in the neoclassical radial electric field. The match is robust against variations of heating power and line-integrated density, which is partly due to the localisation of fluctuations and partly due to effects of the radial gradient in the E × B velocity profile on the wavenumber–frequency spectrum. The latter effect is studied with a newly built synthetic PCI diagnostic and global gyrokinetic simulations with GENE-3D.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Dissipation measures in weakly collisional plasmas

ABSTRACT The physical foundations of the dissipation of energy and the associated heating in weakly collisional plasmas are poorly understood. Here, we compare and contrast several measures that have been used to characterize energy dissipation and kinetic-scale conversion in plasmas by means of a suite of kinetic numerical simulations describing both magnetic reconnection and decaying plasma turbulence. We adopt three different numerical codes that can also include interparticle collisions: the fully kinetic particle-in-cell vpic, the fully kinetic continuum Gkeyll, and the Eulerian Hybrid Vlasov–Maxwell (HVM) code. We differentiate between (i) four energy-based parameters, whose definition is related to energy transfer in a fluid description of a plasma, and (ii) four distribution function-based parameters, requiring knowledge of the particle velocity distribution function. There is an overall agreement between the dissipation measures obtained in the PIC and continuum reconnection simulations, with slight differences due to the presence/absence of secondary islands in the two simulations. There are also many qualitative similarities between the signatures in the reconnection simulations and the self-consistent current sheets that form in turbulence, although the latter exhibits significant variations compared to the reconnection results. All the parameters confirm that dissipation occurs close to regions of intense magnetic stresses, thus exhibiting local correlation. The distribution function-based measures show a broader width compared to energy-based proxies, suggesting that energy transfer is co-localized at coherent structures, but can affect the particle distribution function in wider regions. The effect of interparticle collisions on these parameters is finally discussed.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Surface Water Disinfection Byproducts and Organic Matter Characterization Data Associated with: “Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream”

This dataset is associated with the publication “Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream” published in Water Research X (Leonard et al. 2022; https://doi.org/10.1016/j.wroa.2022.100144). The associated study analyzed temporal trends from the Town of Crested Butte water treatment facility and synoptic sampling at Coal Creek in Crested Butte, Colorado, US. This work demonstrates how drinking water quality archives combined with synoptic sampling and targeted analyses can be used to identify and understand export control points for dissolved organic matter. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) metadata and international geo-sample number (IGSN) mapping file; (4) dissolved organic carbon (DOC), ultraviolet absorbance at 254 nanometers (UV254), total nitrogen (TN), and specific ultraviolet absorbance (SUVA) data; (5) disinfection bioproduct formation potential (DBP-FP) data; (6) readme; (7) methods codes; (8) water collection protocol; (9) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory); and (10) folder of excitation emissions matrix (EEM) spectra. The FTICR folder contains a file of DOC (measured as non-purgeable organic carbon; NPOC) used for FTICR sample preparation. The FTICR folder also contains three subfolders: one subfolder containing the raw .xml data files, one containing the processed data, and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .dat, .R, .ref, or .xml

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Area 6 Control Point: An Architectural Survey of the Area 6 Control Point, Nevada National Security Site, Nye County, Nevada

The U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) proposes to demolish five buildings and five accessory resources in the Area 6 Control Point at the Nevada National Security Site (NNSS) in Nye County, Nevada. The demolition and removal of the buildings and accessories constitute an undertaking subject to review under Section 106 of the National Historic Preservation Act (NHPA) (54 United States Code [USC] § 306101) and its implementing regulations, 36 Code of Federal Regulations (CFR) Part 800. The buildings and accessories were recorded in Identification and Evaluation of 14 Architectural Resources Scheduled for Demolition, Area 6 Control Point and Vicinity, Nevada National Security Site, Nye County, Nevada (Menocal et al. 2020). The report found that the five buildings were not individually eligible for listing in the National Register of Historic Places (NRHP, National Register) but were potentially eligible as contributing elements to an unrecorded Area 6 Control Point district. The report also found that the five accessory resources were not individually eligible for the NRHP but they contributed to other historic properties, including the contributing elements to the unrecorded district. Finally, the report found that the undertaking would result in an adverse effect to historic properties. The State Historic Preservation Office (SHPO) concurred with the report’s findings regarding the eligibility of the buildings and structures in the Area of Potential Effect (APE) and that the undertaking would result in an adverse effect (Reed 2020). The NNSA/NFO, in consultation with the SHPO, then developed the Memorandum of Agreement DE-GM58-21NA25543 Between the U.S. Department of Energy and the Nevada State Historic Preservation Officer Regarding Demolition of Fourteen Buildings and Structures in Area 6 of the Nevada National Security Site, Nye County, hereafter referred to as the MOA. The MOA stipulates that a district boundary be delineated with an accompanying boundary report and supporting photographs (Stipulation III.A) followed by an architectural survey of the potential historic district (Stipulation III.B). The SHPO reviewed and concurred with the proposed district boundary and accompanying boundary report and photographs (O’Neill et al. 2021) on August 23, 2021, in fulfillment of Stipulation III.A (Reed 2021). This architectural survey report has been prepared in accordance with Stipulation III.B. It includes an NRHP evaluation of the district, identifies contributing and non-contributing elements, and is accompanied by Architectural Resource Assessment (ARA) forms. The NRHP evaluation concludes that the Area 6 Control Point is recommended eligible as a historic district under the Secretary of the Interior’s Significance Criterion A at the national level as the location of the command center and various support facilities directly related to timing and firing operations for nuclear testing on the NNSS from 1951 to 1992. It is also recommended eligible under Significance Criterion C for embodying the distinctive characteristics of a nuclear command center in the context of the Cold War and as a significant and distinguishable entity. There are a total of 29 primary resources within the district boundary. Of these, 28 are recommended as contributing elements to the Area 6 Control Point Historic District and one is recommended as non-contributing.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Determination of the mean energy of fast electron losses and anisotropies through thick-target emission on WEST

Abstract A new method to obtain the mean energy of fast electron losses in fusion plasmas using a versatile multi-energy hard x-ray (HXR) detector is presented. The method is based on measuring the thick-target emission of tungsten in the divertor region produced by fast electron losses interacting with the target and modeling the tungsten spectra by a Monte Carlo code which simulates the interaction between a beam of electrons and a solid target. The mean energy of the fast electron losses is determined through the comparison between the experimental and synthetic emission. The results show that fast electron losses during lower hybrid current drive discharges at WEST have a mean energy of 90–140 keV and represent only 2% of the total heat flux at the target. Additionally, anisotropic HXR emission has been detected for the first time at the WEST core and edge plasma, with opposite directions. It is due to the forward-peak emission of two distinctive populations of fast electrons: co-current fast electrons in the core and counter-current fast electron losses at the inner strike point. In view of future experiments like ITER where electron cyclotron current drive will generate a fast electron population, this technique could serve as a real-time monitor of fast electron losses and eventually feed an actuator on the current drive generation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Gyrokinetic analysis of inter-edge localized mode transport mechanisms in a DIII-D pedestal

In this study, gyrokinetic simulations are used to study pedestal fluctuations for DIII-D discharge 174082 using the GENE code. Nonlinear local simulations indicate that electron heat flux has contributions from electron temperature gradient-driven transport but at levels insufficient to satisfy power balance. We show that microtearing modes (MTM) and neoclassical transport are likely to account for the remaining observed energy losses in the electron and ion channels, respectively. The MTM instabilities found in the simulations are consistent with the high-frequency fluctuations identified in the magnetic fluctuation data from Mirnov coils. The fluctuation data in this discharge also exhibit a low-frequency band of fluctuations. By modifying the equilibrium profiles and plasma β, simulations produce MHD modes, which may be responsible for these observed low-frequency fluctuations. We compare several metrics involving ratios of fluctuation amplitudes and transport quantities for both MTMs and MHD modes. This analysis suggests that the available data are consistent with the simultaneous activity of both MHD modes and MTMs provided that the former is limited largely to the particle transport channel.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Nonlinear MHD modeling of n = 1 RMP -induced pedestal transport and mode coupling effects on ELM suppression in KSTAR

We report fully suppressing edge-localized modes (ELMs), e.g., with resonant magnetic perturbations (RMPs), is essential to reach and sustain high-performance steady-state H-mode plasmas because large ELMs can significantly reduce the lifetime of divertor components in future tokamak reactors. RMP-driven ELM suppression in KSTAR has been modeled by coupling the neoclassical transport code PENTRC to the nonlinear 3D MHD code JOREK. We have found that the radial transport from the combined effects of the kink-peeling, tearing response, and neoclassical toroidal viscosity can explain the pedestal degradation observed in experiments. In addition, it has been found that the RMP response can increase the inter-ELM heat flux on the lower outer divertor by redistributing the heat transport between the divertor plates. In addition to the degraded pedestal, ELM suppression is also attributable to the RMP-induced mode interactions. While the linear stability of peeling-ballooning mode (PBMs) improves owing to the degraded pedestal, the PBM and RMP interaction increases the spectral transfer between edge harmonics, preventing catastrophic growth and the crash of unstable modes. Here, it turns out that the magnetic islands near the pedestal top can play a vital role in mediating the mode interactions.

mode coupling↗

DOE OSTI2022

Development of a synthetic phase contrast imaging diagnostic for turbulence studies at Wendelstein 7-X

Abstract We present a synthetic phase contrast imaging (PCI) diagnostic for studying turbulence at the Wendelstein 7-X (W7-X) stellarator. We first describe the implemented instrument response model, which captures diffraction effects, detector noise, and the long-wavelength cutoff due to the phase plate of the PCI system. To verify the instrument response model, we show that it is capable of reproducing the PCI signal generated by the sound wave speaker used for calibration at W7-X. Next, we discuss the calculation of synthetic PCI signals based on the global, nonlinear gyrokinetic codes GENE-3D and EUTERPE, including results from some of the first stellarator simulations of this type with kinetic electrons (KEs) in GENE-3D. While the simulations used in this work lack a neoclassical radial electric field, which is crucial for reproducing experimental PCI signals, they do indicate that the dominant rotation direction and velocities of the turbulent fluctuations can be inferred from the wave number-frequency spectra of the PCI signals, as expected. The synthetic PCI wave number spectra are further shown to be similar to those of the line-integrated fluctuating electron density, with distinct differences between adiabatic and KE simulations, explainable by previously published turbulence models. For example, the wave number spectra of all adiabatic electron simulations analyzed here follow a power law with an exponent close to −5 for sufficiently large wave numbers. This indicates that universal features of electron density turbulence at W7-X may be studied using the PCI system.

EUTERPE↗

DOE OSTI2020

SN 2018fif: The Explosion of a Large Red Supergiant Discovered in Its Infancy by the Zwicky Transient Facility

High-cadence transient surveys are able to capture supernovae closer to their first light than ever before. Applying analytical models to such early emission, we can constrain the progenitor stars' properties. Here, we present observations of SN 2018fif (ZTF 18abokyfk). The supernova was discovered close to first light and monitored by the Zwicky Transient Facility (ZTF) and the Neil Gehrels Swift Observatory. Early spectroscopic observations suggest that the progenitor of SN 2018fif was surrounded by relatively small amounts of circumstellar material compared to all previous cases. This particularity, coupled with the high-cadence multiple-band coverage, makes it a good candidate to investigate using shock-cooling models. We employ the SOPRANOS code, an implementation of the model by Sapir & Waxman and its extension to early times by Morag et al. Compared with previous implementations, SOPRANOS has the advantage of including a careful account of the limited temporal validity domain of the shock-cooling model as well as allowing usage of the entirety of the early UV data. We find that the progenitor of SN 2018fif was a large red supergiant with a radius of $R={744.0}_{-128.0}^{+183.0}\,{R}_{\odot }$ and an ejected mass of ${M}_{\mathrm{ej}}={9.3}_{-5.8}^{+0.4}\,{M}_{\odot }$. Our model also gives information on the explosion epoch, the progenitor's inner structure, the shock velocity, and the extinction. The distribution of radii is double-peaked, with smaller radii corresponding to lower values of the extinction, earlier recombination times, and a better match to the early UV data. If these correlations persist in future objects, denser spectroscopic monitoring constraining the time of recombination, as well as accurate UV observations (e.g., with ULTRASAT), will help break the extinction/radius degeneracy and independently determine both.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Data and Scripts Associated with the Manuscript “Water Column Respiration in the Yakima River Basin is Explained by Temperature, Nutrients and Suspended Solids”

This data package is associated with the publication “Water Column Respiration in the Yakima River Basin is Explained by Temperature, Nutrients and Suspended Solids” published in EGU Biogeochemistry (Laan et al. 2025). In this research, water column respiration (ERwc) data, surface water chemistry data, organic matter (OM) chemistry data, and publicly available geospatial data were used in analysis to evaluate the variability in ERwc at 47 sites across the Yakima River basin in Washington, USA. In addition to this readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. The data package includes the data inputs, and outputs, and R scripts to reproduce all the analyses performed in the manuscript and create manuscript figures. The data package is comprised of three main folders (Code, Data, and Figures). The Code folder is comprised of four scripts and three analysis-specific subfolders that contain the R scripts to perform the analyses described in the publication and create publication figures. The Data folder is comprised of two “.csv” files and four subfolders that contain data input and output files. The Published_Data folder contains a readme that directs the user to download the appropriate files and add to this folder when using scripts. The Figures folder includes figures from the manuscript in “.pdf” and “.png” formats and a folder with intermediate figure files. This data package is associated with a GitHub repository which can be found at https://github.com/river-corridors-sfa/rcsfa-RC2-SPS-ERwc. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

Thermoflexus hugenholtzii JAD2 T , the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2 T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13 C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2 T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2 T using 13 C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13 C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Urban relatives ameliorate survival disparities for genitourinary cancer in rural patients

Patients living in rural areas have worse cancer-specific outcomes. This study examines the effect of family-based social capital on genitourinary cancer survival. We hypothesized that rural patients with urban relatives have improved survival relative to rural patients without urban family. We examined rural and urban based Utah individuals diagnosed with genitourinary cancers between 1968 and 2018. Familial networks were determined using the Utah Population Database. Patients and relatives were classified as rural or urban based on 2010 rural–urban commuting area codes. Overall survival was analyzed using Cox proportional hazards models. We identified 24,746 patients with genitourinary cancer with a median follow-up of 8.72 years. Rural cancer patients without an urban relative had the worst outcomes with cancer-specific survival hazard ratios (HRs) at 5 and 10 years of 1.33 (95% CI 1.10–1.62) and 1.46 (95% CI 1.24–1.73), respectively relative to urban patients. Rural patients with urban first-degree relatives had improved survival with 5- and 10-year survival HRs of 1.21 (95% CI 1.06–1.40) and 1.16 (95% CI 1.03–1.31), respectively. Our findings suggest rural patients who have been diagnosed with a genitourinary cancer have improved survival when having relatives in urban centers relative to rural patients without urban relatives. Further research is needed to better understand the mechanisms through which having an urban family member contributes to improved cancer outcomes for rural patients. Better characterization of this affect may help inform policies to reduce urban–rural cancer disparities.

60 APPLIED LIFE SCIENCES↗