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At least 847 records · Page 47

When do different scenarios of projected electricity demand start to meaningfully diverge?

Resource adequacy studies look at balancing electricity supply and demand on 10- to 15-year time horizons while asset investment planning typically evaluates returns on 20- to 40-year time horizons. Projections of electricity demand are factored into the decision-making in both cases. Climate, energy policy, and socioeconomic changes are key uncertainties known to influence electricity demands, but their relative importance for demands over the next 10-40 years is unclear. The power sector would benefit from a better understanding of the need to characterize these uncertainties for resource adequacy and investment planning. In this study, we quantify when projected United States (U.S.) electricity demands start to meaningfully diverge in response to a range of climate, energy policy, and socioeconomic drivers. Here we use a wide yet plausible range of 21st century scenarios for the U.S. The projections span two population/economic growth scenarios (Shared Socioeconomic Pathways 3 and 5) and two climate/energy policy scenarios, one including climate mitigation policies and one without (Representative Concentration Pathways 4.5 and 8.5). Each climate/energy policy scenario has two warming levels to reflect a range of climate model uncertainty. We show that the socioeconomic scenario matters almost immediately – within the next 10 years, the climate/policy scenario matters within 25-30 years, and the climate model uncertainty matters only after 50+ years. This work can inform the power sector working to integrate climate change uncertainties into their decision-making.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Detection efficiency measurement and operational tests of the X-Arapuca for the first module of DUNE far detector

The Deep Underground Neutrino Experiment (DUNE) is a dual-site experiment for long-baseline neutrino oscillation studies, able to resolve the neutrino mass hierarchy and measure δ$_{CP}$. DUNE will also have sensitivity to supernova neutrinos and to processes beyond the Standard Model, such as nucleon decay searches. The Far Detector (FD) will consist of four liquid argon TPC (17.5 kt total mass) with systems for the detection of charge and scintillation light produced by an ionization event. The charge detection system permits both calorimetry and position determination. In addition, the photon-detection system (PDS) enhances the detector capabilities for all DUNE physics drivers. The PDS of the first FD module consists of light collector modules placed in the inactive space between the innermost wire planes of the TPC anode. The light collectors, the so-called X-ARAPUCAS, are functionally a light trap that captures wavelength-shifted photons inside boxes with highly reflective internal surfaces where they are guided to Silicon Photo-multipliers (SiPM) by wavelength-shifting (WLS) bars. Functionality and operational tests of the X-ARAPUCAS to be installed in ProtoDUNE-SP phase II (FD DUNE prototype at the scale 1:20), as well as the measurement of their absolute detection efficiency is reported in this publication.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Modeling Rate Dependent Volume Change in Porous Electrodes in Lithium-Ion Batteries

Automotive manufacturers are working to improve individual cell, module, and overall pack design by increasing the performance, range, and durability, while reducing cost. One key piece to consider during the design process is the active material volume change, its linkage to the particle, electrode, and cell level volume changes, and the interplay with structural components in the rechargeable energy storage system. As the time from initial design to manufacture of electric vehicles decreases, design work needs to move to the virtual domain; therefore, a need for coupled electrochemical-mechanical models that take into account the active material volume change and the rate dependence of this volume change need to be considered. In this study, we illustrated the applicability of a coupled electrochemical-mechanical battery model considering multiple representative particles to capture experimentally measured rate dependent reversible volume change at the cell level through the use of an electrochemical-mechanical battery model that couples the particle, electrode, and cell level volume changes. By employing this coupled approach, the importance of considering multiple active material particle sizes representative of the distribution is demonstrated. The non-uniformity in utilization between two different size particles as well as the significant spatial non-uniformity in the radial direction of the larger particles is the primary driver of the rate dependent characteristics of the volume change at the electrode and cell level.

Electrochemistry↗

Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science

Disturbances fundamentally alter ecosystem functions, yet predicting their impacts remains a key scientific challenge. While the study of disturbances is ubiquitous across many ecological disciplines, there is no agreed-upon, cross-disciplinary foundation for discussing or quantifying the complexity of disturbances, and no consistent terminology or methodologies exist. This inconsistency presents an increasingly urgent challenge due to accelerating global change and the threat of interacting disturbances that can destabilize ecosystem responses. By harvesting the expertise of an interdisciplinary cohort of contributors spanning 42 institutions across 15 countries, we identified an essential limitation in disturbance ecology: the word ‘disturbance’ is used interchangeably to refer to both the events that cause, and the consequences of, ecological change, despite fundamental distinctions between the two meanings. In response, we developed a generalizable framework of ecosystem disturbances, providing a well-defined lexicon for understanding disturbances across perspectives and scales. The framework results from ideas that resonate across multiple scientific disciplines and provides a baseline standard to compare disturbances across fields. This framework can be supplemented by discipline-specific variables to provide maximum benefit to both inter- and intra-disciplinary research. To support future syntheses and meta-analyses of disturbance research, we also encourage researchers to be explicit in how they define disturbance drivers and impacts, and we recommend minimum reporting standards that are applicable regardless of scale. Finally, we discuss the primary factors we considered when developing a baseline framework and propose four future directions to advance our interdisciplinary understanding of disturbances and their social-ecological impacts: integrating across ecological scales, understanding disturbance interactions, establishing baselines and trajectories, and developing process-based models and ecological forecasting initiatives. Our experience through this process motivates us to encourage the wider scientific community to continue to explore new approaches for leveraging Open Science principles in generating creative and multidisciplinary ideas.

54 ENVIRONMENTAL SCIENCES↗

Organic matter sulfurization and organic carbon burial in the Mesoproterozoic

Throughout the Proterozoic Era, sedimentary organic carbon burial helped set the pace of global oxygenation and acted as a major modulator of atmospheric CO 2 and climate. Although Proterozoic rocks generally contain low concentrations of organic matter (OM), there are key exceptions to this rule, including the relatively OM-rich Arctic Bay shales from Baffin Island, Canada (Bylot Supergroup, Borden Basin, ~1.05 Ga). The mechanisms driving elevated OM concentrations in these and other Proterozoic shales remain poorly understood. In the Mesozoic and Cenozoic, organic matter sulfurization can be a major driver of enhanced OM burial across a range of redox conditions comparable to those inferred for many Proterozoic environments. Therefore, in this study, we evaluate the role of sulfurization in driving OM preservation in the Mesoproterozoic Borden Basin and discuss its relevance to Proterozoic systems in general. We present the first evidence for syngenetic-to-early-diagenetic OM sulfurization in a Proterozoic basin, which begins to fill a several-billion-year gap in our record of organic S across Earth history. We find that OM sulfurization was particularly extensive in shales from a relatively shallow-water section (Alpha River) but less extensive in shales deposited in deeper water (Shale Valley), which is consistent with models that infer sulfidic ‘wedges’ or O 2 -minimum-zone-type structures on shelf margins at least intermittently at this time. At the shallower site, organic S and pyrite are similarly 34 S-depleted and thus likely formed at roughly the same time near the sediment–water interface under conditions previously interpreted to have been ferruginous to intermittently sulfidic. In contrast, at the deeper-water site, large S-isotope differences between pyrite and organic S along with low apparent OM sulfurization intensities indicate that pyrite formation was favored over OM sulfurization during early sedimentation under variable but primarily ferruginous conditions. Although Mesoproterozoic biomass can be substantially sulfurized, indicators of sulfurization intensity are not correlated with OM concentrations, and therefore sulfurization does not appear to have been the primary driver of enhanced OM concentrations in Arctic Bay Formation shales. The link between sulfurization and total OM preservation may have been modulated during the deposition of Arctic Bay Formation shales by differences in iron availability, nutrient cycling, and particle dynamics in the Mesoproterozoic.

58 GEOSCIENCES↗

Microsimulation of Energy and Flow Effects from Optimal Automated Driving in Mixed Traffic

In this paper we study the energy and traffic impact of a proposed Anticipative Cruise Controller in a PTV VISSIM microsimulation environment. We dissect our controller into two parts: 1. the unconnected mode, active when following a human-driven vehicle, and 2. the connected mode, active when following another automated vehicle equipped with connectivity. Probabilistic constraints balance safety considerations with inter-vehicle compactness, and vehicle constraints for acceleration capabilities are expressed through the use of powertrain maps. Emergent highway traffic scenarios are then modeled using time headway distributions from empirical traffic data. To study the impact of automation over a range of demands of free-flow to stop-and-go, we vary vehicle flux from low to high and vary automated vehicle penetration from low to high. When examining all-human driving scenarios, network capacity failed to meet demand in high-volume scenarios, such as rush-hour traffic. We further find that with connected automated vehicles introduced, network capacity was improved to support the high-volume scenarios. Finally, we examine energy efficiencies of the fleet for conventional, electric, and hybrid vehicles. We find that automated vehicles perform at a 10%-20% higher energy efficiency over human drivers when considering conventional powertrains, and find that automated vehicles perform at a 3%-9% higher energy efficiency over human drivers when considering electric and hybrid powertrains. Due to secondary effects of smoothing traffic flow and reducing unnecessary braking, energy benefits also apply to human-driven vehicles that interact with automated ones. Such simulated humans were found to drive up to 10% more energy-efficiently than they did in the baseline all-human scenario.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Analyzing historical snow trends in interior Alaska

Study region The Chena River watershed in Interior Alaska, USA Study focus This study examines 40 years (water years 1982–2021) of snowpack characteristics to consider its hydrological implications in the 5350 km² Chena River basin. Using observations and a fine-scale physics model, we analyzed trends of snow water equivalent (SWE), snow onset and disappearance, and snow cover duration (SCD). New hydrological insights for the region Results indicate a decline in SWE across the modeled domain, averaging a decrease of 3 mm per decade, with larger decreases (up to 10 mm per decade) at lower elevations. While domain-averaged SWE trends were not statistically significant, observed SCD showed statistically significant decreases: −5.2, −5.0, and −4.4 days per decade at Teuchet Creek, Fairbanks F.O., and Little Chena Ridge, respectively. Notably, observations at SNOTEL stations and modeling revealed no statistically significant change in domain-averaged Rain-on-Snow (ROS) events over the 40-year period, contrasting some regional future estimates of increased ROS frequency. Peak streamflow did not consistently correlate with peak SWE levels, suggesting that other environmental factors such as ROS events and rapid temperature increases (e.g., a 10°C spike observed in 1992) are key drivers of hydrological outcomes. These findings improve understanding of complex subarctic hydrological processes impacting permafrost and highlight the need for adaptive water resource management to mitigate multi-factor risks like flooding and wildfire, requiring proactive planning.

54 ENVIRONMENTAL SCIENCES↗

Bias-Modulated ALD of ZnO: Insights into Precursor-Surface Interactions for ZnO Films

Atomic layer deposition (ALD) is widely used to deposit conformal thin films but is often limited in the tunability of the resulting material’s properties. Substrate bias and electric fields alter precursor-surface interactions and provide means to tune material properties. To explore this, we performed zinc oxide (ZnO) ALD using diethylzinc (DEZ) and water on silicon native oxide substrates at 150 °C in a sample holder designed to create a static electrical field by biasing one plate of a parallel plate capacitor-style sample holder during deposition. ZnO films prepared in an electric field/on a biased sample holder were thinner, changed relative crystalline composition, and contained more carbon compared to samples grown in identical sample holders without bias. The thickness was independent of the magnitude of the eletric field between plates, indicating that the primary driver for the change was substrate biasing not the electric field between plates of the parallel plate capacitor-style sample holder. Density functional theory calculations showed enhanced electron migration between dissociatively adsorbed DEZ molecules and the ZnO (002) facet with increasing force from an electric field at the substrate surface, which strengthens the electronic interactions between the surface and the adsorbate. These models offer a compelling explanation for the inhibited growth, changes in the crystallinity, and increase in carbon content of films grown in an electric field/on biased plates.

Jones, Jessica C. (ORCID:0000000174754620)↗

Gamma Source Verification for GAMSRC and GAMSOR

Nuclear reactors that rely upon the fission reaction have two modes of thermal energy deposition in the reactor system: neutron absorption and gamma absorption. The gamma rays are typically generated by neutron capture reactions or during the fission process which means the primary driver of energy production is of course the neutron interactions. The GAMSOR program was first built in the mid 1980s to properly account for the gamma heating in an operating reactor core on core internals. The GAMSOR code is sequence of DIF3D calculations to compute the neutron and gamma flux and combine them to define both the neutron and gamma heating throughout the modeled domain. The goal of this manuscript is to present the software verification of GAMSOR. The first step of the GAMSOR sequence of calculations involves of a modified version of DIF3D (called DIF3D-GAMSOR) which generates a gamma source distribution for the follow-on DIF3D gamma transport calculation (step 2). This modified version of DIF3D increases the burden of maintenance and verification work on GAMSOR as one must reverify the DIF3D capabilities which is undesirable. Because the calculation of the gamma source is the only unique aspect of GAMSOR beyond the regular DIF3D capabilities, that part was put in a standalone code called GAMSRC such that one can use the verified DIF3D code in step 1 followed by GAMSRC to carry out the same GAMSOR calculation step. As a consequence, this manuscript is focused on verification of the gamma source files generated by GAMSRC. The verification of the modified version of DIF3D (DIF3D-GAMSOR) will be done less rigorously in that it will be verified that it produces the same output that GAMSRC does and thus GAMSRC is equivalent to GAMSOR on the problems studied here. Hand calculations and independent numerical calculations of the gamma source generation are used for the verification work. This work follows the same methodology of GAMSRC. As expected, the results agree well with those calculated by GAMSRC as will be shown.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Gamma Source Verification for GAMSRC and GAMSOR

Nuclear reactors that rely upon the fission reaction have two modes of thermal energy deposition in the reactor system: neutron absorption and gamma absorption. The gamma rays are typically generated by neutron capture reactions or during the fission process which means the primary driver of energy production is of course the neutron interactions. The GAMSOR program was first built in the mid 1980s to properly account for the gamma heating in an operating reactor core on core internals. The GAMSOR code is sequence of DIF3D calculations to compute the neutron and gamma flux and combine them to define both the neutron and gamma heating throughout the modeled domain. The goal of this manuscript is to present the software verification of GAMSOR. The first step of the GAMSOR sequence of calculations involves of a modified version of DIF3D (called DIF3D-GAMSOR) which generates a gamma source distribution for the follow-on DIF3D gamma transport calculation (step 2). This modified version of DIF3D increases the burden of maintenance and verification work on GAMSOR as one must reverify the DIF3D capabilities which is undesirable. Because the calculation of the gamma source is the only unique aspect of GAMSOR beyond the regular DIF3D capabilities, that part was put in a standalone code called GAMSRC such that one can use the verified DIF3D code in step 1 followed by GAMSRC to carry out the same GAMSOR calculation step. As a consequence, this manuscript is focused on verification of the gamma source files generated by GAMSRC. The verification of the modified version of DIF3D (DIF3D-GAMSOR) will be done less rigorously in that it will be verified that it produces the same output that GAMSRC does and thus GAMSRC is equivalent to GAMSOR on the problems studied here. Hand calculations and independent numerical calculations of the gamma source generation are used for the verification work. This work follows the same methodology of GAMSRC. As expected, the results agree well with those calculated by GAMSRC as will be shown.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort

The drivers of critical coronavirus disease 2019 (COVID-19) remain unknown. Given major confounding factors such as age and comorbidities, true mediators of this condition have remained elusive. We used a multi-omics analysis combined with artificial intelligence in a young patient cohort where major comorbidities were excluded at the onset. The cohort included 47 “critical” (in the intensive care unit under mechanical ventilation) and 25 “non-critical” (in a non-critical care ward) patients with COVID-19 and 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cell proteomics, cytokine profiling, and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing, and structural causal modeling were used. Patients with critical COVID-19 were characterized by exacerbated inflammation, perturbed lymphoid and myeloid compartments, increased coagulation, and viral cell biology. Among differentially expressed genes, we observed up-regulation of the metalloprotease ADAM9. This gene signature was validated in a second independent cohort of 81 critical and 73 recovered patients with COVID-19 and was further confirmed at the transcriptional and protein level and by proteolytic activity. Ex vivo ADAM9 inhibition decreased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, cohort of individuals with COVID-19, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. We further identified ADAM9 as a driver of disease severity and a candidate therapeutic target.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Quantifying the effects of urbanization on floods in a changing environment to promote water security — A case study of two adjacent basins in Texas

The increased occurrence of flood events resulting from urbanization and global climate change is a great threat to water security. To systematically evaluate the impacts of urbanization on floods, here we applied a paired catchments approach to two adjacent river basins in south-central Texas — the San Antonio River Basin (SARB), with fast urbanization; and the Guadalupe River Basin (GRB), with little land cover change. A physics-based distributed hydrological model — the Distributed Hydrology Soil Vegetation Model, embedded with a multi-purpose reservoir module (DHSVM-Res) — was used to simulate streamflow and reservoir storage. The simulations were conducted under different land cover scenarios, including a newly developed continuous land cover series (CLCS). Holistic analyses were then conducted for the paired basins using three methods: analyzing the selected flood events, detecting change points (CP) of monthly floods, and testing the elasticity of long-term flood regimes. The results suggest that: (1) urbanization may reduce lag time and elevate flood peaks significantly by 3–30% in our study area; (2) when there is little land cover change, changing climate is the major driver of variations in the monthly maximum streamflow (MMS); (3) fast urbanization can amplify streamflow variability, increase MMS significantly, and thus alter the timing of CP; and (4) the mean MMS of observed streamflow in the SARB has increased by as much as 75.7% from the pre-CP to post-CP periods. This comprehensive study fills in a gap in our current understanding of the isolated impacts of urbanization on flooding and is expected to support future explorations of anthropogenic influences on floods.

54 ENVIRONMENTAL SCIENCES↗

Model-Based Energy and Cost Analysis of Direct Air Capture Using ePTFE-Based Laminate-Structured Gas–Solid Contactors

Carbon dioxide removal (CDR) technologies will play a significant role in limiting global warming if implemented on a large scale. Direct air capture (DAC) is a scalable approach for removing atmospheric carbon, yet the true scope of its scalability remains unclear due to the early stage of technology development and high first plant costs. This study provides groundwork for understanding the technoeconomic trade-offs in developing DAC systems using laminate-structured gas–solid contactors, encompassing the analysis of both contactor and process design spaces. The robust mass transfer and process models outlined in this study provide tools for evaluating DAC processes and designing DAC plants based on cost and energy analysis. First, the key contactor geometrical parameters are identified to understand the CO 2 productivity–energy demand trade-offs, where geometries yielding higher mass transfer rates can achieve higher CO 2 productivities at the expense of energy consumption by fans and steam use. Next, a detailed process parametric study is conducted for DAC systems coupled with steam-assisted temperature-vacuum swing adsorption (S-TVSA) to visualize the trade-offs in the multidimensional design space. The main cost driver dramatically changes over different process conditions, but the operating cost prevailed on the Pareto front, with potential to operate as low as 150 $/tonne-CO 2 (within the cost range of 148–504 $/tonne-CO 2 in this study where the DAC system is coupled with industrial facilities for steam production).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monitoring Methane Emissions from Oil and Gas Operations

The atmospheric concentration of methane has more than doubled since the start of the Industrial Revolution. Methane is the second-most-abundant greenhouse gas created by human activities and a major driver of climate change. This APS-Optica report provides a technical assessment of the current state of monitoring U.S. methane emissions from oil and gas operations, which accounts for roughly 30% of U.S. anthropogenic methane emissions. The report identifies current technological and policy gaps and makes recommendations for the federal government in three key areas: methane emissions detection, reliable and systematized data and models to support mitigation measures, and effective regulation.

02 PETROLEUM↗

From Deposition to Encapsulation: Roll-to-roll manufacturing of organic light emitting devices for lighting (Final Report)

Organic light emitting devices (OLEDs) are promising solid state light sources due to their high efficiency, high color quality and flexible form factors. The key to enable low cost OLED lighting, is to rapidly fabricate thin film organic layers on a continuous flexible roll, called R2R processing. This project aims to investigate the feasibility of mass production of OLED lighting using the R2R process, from deposition to encapsulation. A high efficiency white OLED is fabricated on 10 cm-wide substrate rolls in a pilot R2R tool comprising of two different organic deposition: vacuum thermal evaporation (VTE) and organic vapor phase deposition (OVPD). A high quality encapsulation process to package OLEDs is demonstrated using an atomic layer deposition tool integrated to the R2R system without air exposure. The method to achieve ultrahigh deposition rates required by R2R processing is demonstrated by OVPD. Uniform organic semiconductor thin films grown by OVPD at rates as high as 50 Å/s are achieved. A comprehensive numerical model that is capable of simulating complex, multilayer WOLED structures is developed to provide an alternative to experimental iterations of OLED design and tests. A cost estimate on the R2R production of WOLEDs for lighting is developed. Assuming a WOLED luminance of 10 klm/m 2 , the cost of a WOLED light engine is anticipated to be $\$ 12.5$ /klm. With incremental reduction in material and driver costs and improved luminance, the cost of WOLED lighting can be reduced to $\$ 6.3$ /klm in the near term. These findings suggest OLED lighting can be volume manufactured by R2R vapor deposition methods with much reduced costs compared to current batch processing methods, potentially positioning WOLEDs for use in numerous premium lighting applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Editorial: Plant-Soil Interactions Under Changing Climate

The health and well-being of plants and soil is crucial for all life on Earth. It is well-known that vegetation cover follows climatic zones, and plants respond to climatic drivers such as temperature and precipitation. It is also well-known that plant health depends on the properties and health of the soil, and that strong interactions among biota above and belowground dictate the functioning of both realms. Yet, soils and the processes occurring belowground are often considered a “black box,” and are treated very simplistically in our efforts to understand, quantify, and model the future of the planet. Our understanding of the interactions between plants and soils is also far from complete and offers some of the most important research frontiers in community ecology, biogeochemistry, and global change science.

59 BASIC BIOLOGICAL SCIENCES↗

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants ( Panicum virgatum ) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

54 ENVIRONMENTAL SCIENCES↗

RatXcan: A framework for cross-species integration of genome-wide association and gene expression data

Genome-wide association studies (GWAS) have implicated specific alleles and genes as risk factors for numerous complex traits. However, translating GWAS results into biologically and therapeutically meaningful discoveries remains extremely challenging. Most GWAS results identify noncoding regions of the genome, suggesting that differences in gene regulation are the major driver of trait variability. To better integrate GWAS results with gene regulatory polymorphisms, we previously developed PrediXcan (also known as “transcriptome-wide association studies” orTWAS), which maps SNPs to predicted gene expression using GWAS data. In this study, we developed RatXcan, a framework that extends this methodology to outbred heterogeneous stock (HS) rats. RatXcan accounts for the close familial relationships among HS rats by modeling the relatedness with a random effect that encodes the genetic relatedness. RatXcan also corrects for polygenic-driven inflation because of the equivalence between a relatedness random effect and the infinitesimal polygenic model. To develop RatXcan, we trained transcript predictors for 8,934 genes using reference genotype and expression data from five rat brain regions. We found that the cis genetic architecture of gene expression in both rats and humans was sparse and similar across brain tissues. We tested the association between predicted expression in rats and two example traits (body length and BMI) using phenotype and genotype data from 5,401 densely genotyped HS rats and identified a significant enrichment between the genes associated with rat and human body length and BMI. Thus, RatXcan represents a valuable tool for identifying the relationship between gene expression and phenotypes across species and paves the way to explore shared biological mechanisms of complex traits.

Genetics & Heredity↗