Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “relational database”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cognitive simulation models for inertial confinement fusion: Combining simulation and experimental data

The design space for inertial confinement fusion (ICF) experiments is vast, and experiments are extremely expensive. Researchers rely heavily on computer simulations to explore the design space in search of high-performing implosions. However, ICF multiphysics codes must make simplifying assumptions, and thus deviate from experimental measurements for complex implosions. For more effective design and investigation, simulations require input from past experimental data to better predict future performance. In this work, we describe a cognitive simulation method for combining simulation and experimental data into a common, predictive model. This method leverages a machine learning technique called “transfer learning,” the process of taking a model trained to solve one task, and partially retraining it on a sparse dataset to solve a different, but related task. In the context of ICF design, neural network models are trained on large simulation databases and partially retrained on experimental data, producing models that are far more accurate than simulations alone. Here, we demonstrate improved model performance for a range of ICF experiments at the National Ignition Facility and predict the outcome of recent experiments with less than 10% error for several key observables. We discuss how the methods might be used to carry out a data-driven experimental campaign to optimize performance, illustrating the key product—models that become increasingly accurate as data are acquired.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Theoretical Multinary Perovskite Oxides Dataset

Perovskite oxides (ternary chemical formula ABO3) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, the AA'BB'O6 compositions were generated in the a-b+a- Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with DFT using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔHf) and decomposition enthalpies (ΔHd) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated AA'BB'O6 perovskite structures using MP-compatible DFT calculations

Bare, Zachary↗
DOE OSTI2024

Unveiling the Essential Parameters Driving Mineral Reactions during CO2 Storage in Carbonate Aquifers through Proxy Models

Numerical simulation is a commonly employed technique for studying carbon dioxide (CO2) storage processes in porous media, particularly saline aquifers. It enables the representation of diverse trapping mechanisms and the assessment of CO2 retention capacity within the subsurface. The intricate physicochemical phenomena involved necessitate the incorporation of multiphase flow, accurate depiction of fluid and rock properties, and their interactions. Among these factors, geochemical reaction rates and mechanisms are pivotal for successful CO2 trapping in carbonate reactive rocks. However, research on kinetic parameters and the influence of lithology on CO2 storage remains limited. This limitation is partly due to the challenges faced in laboratory experiments, where the time scale of the reactions and the lack of in situ conditions hinder accurate measurement of mineral reaction rates. This study employs proxy models constructed using response surfaces calibrated with simulation results to address uncertainties associated with geochemical reactions. Monte Carlo simulation is utilized to explore a broader range of parameters and identify influential factors affecting CO2 mineralization. The findings indicate that an open database containing kinetic parameters can support uncertainty assessment. Additionally, the proxy models effectively represent objective functions related to CO2 injectivity and mineralization, with calcite dissolution playing a predominant role. pH, calcite concentration, and CO2 injection rate significantly impact dolomite precipitation, while quartz content remains unaffected.

58 GEOSCIENCES↗
DOE OSTI2020

Linking Pharmacogenomic Information on Drug Safety and Efficacy with Ethnic Minority Populations

Numerous prescription drugs’ labeling contains pharmacogenomic (PGx) information to aid health providers and patients in the safe and effective use of drugs. However, clinical studies for such PGx biomarkers and related drug doses are generally not conducted in diverse ethnic populations. Thus, it is urgently important to incorporate PGx information with genetic characteristics of racial and ethnic minority populations and utilize it to promote minority health. In this project a bioinformatics approach was developed to enhance the collection of PGx information related to ethnic minorities to pave the way toward understanding the population-wide utility of PGx information. To address this challenge, we first gathered PGx information from drug labels. Second, we extracted data on the allele frequency information of genetic variants in ethnic minority groups from public resources. Then, we collected published research articles on PGx biomarkers and related drugs for reference. Finally, the data were integrated and formatted to build a new PGx database containing information on known drugs and biomarkers for ethnic minority groups. This database provides scientific information needed to evaluate available PGx information to enhance drug dose selection and drug safety for ethnic minority populations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Carbon Storage Site Mapping Inquiry Tool (MapIT)

To date, 48 projects, consisting of 139 wells, are currently under review with the Environmental Protection Agency’s (EPA) Underground Injection Control (UIC) Program for Class VI – wells used for geologic sequestration of carbon dioxide. The number of applications submitted is expected to increase in coming years with the increase of the 45Q tax credit available to projects that initiate construction prior to 2033. The amount of data collected to submit a Class VI permit is vast, and often disparate, coming from state, federal, and commercial entities, as well as field-specific data collected within an area of interest. When preparing for site selection and permitting, the initial aggregation of relevant public data can be time intensive. The Carbon Storage Site Mapping Inquiry tool (MapIT) was created to support and accelerate the discovery and accessibility of open-source data and information available across the USA. Data was aggregated and organized based on data types described within the EPA UIC Class VI permit documentation. The online tool enables users to explore hundreds of geospatial data layers and connect to additional external resources, leveraging API and REST services where possible to ensure updates to data in real time. MapIT enables users to explore state and federal data related to geologic, geophysical, structural, hydrologic, and contextual information. In addition to displaying spatial data and linking to external resources, MapIT leverages custom widgets to ensure that internal data and external data are discoverable and accessible. The widgets connect users to resources such as the USGS publications and the USGS Earthquake Catalog based on a user-defined location. This talk will describe data aggregation workflows, data types, data preparation, and tool development for MapIT. The Carbon Storage Site Mapping Inquiry Tool and underlying database are valuable, intuitive resources that empower government, academic, commercial and industry stakeholders to explore, analyze, and acquire carbon storage related data.

Morkner, Paige↗
DOE OSTI2020

Development of a Comprehensive Two-Phase Flow Database for the Validation of NEK-2P

Three-dimensional (3-D) two-phase Computational Fluid Dynamics (CFD) codes are emerging as a powerful and potentially practical tool for applications in which detailed local flow information is needed. However, two-phase flow models and associated closure relations are not well established for CFD applications, which is partly due to the lack of high-quality validation data. The main objective of this work is to develop a comprehensive database of two-phase flows that can be used to validate two-phase CFD codes such as NEK-2P. In this project, four advanced local measurement systems, including Particle Image Velocimetry and Planar Laser-Induced Fluorescence (PIV-PLIF), high-speed imaging, x-ray densitometry, and multi-sensor conductivity probe are employed to measure the local two-phase flow parameters of both gas and liquid phases. By combining these techniques, the local void fraction, bubble velocity, interfacial area concentration, bubble frequency, liquid velocity, turbulence intensity, etc., in various two-phase flow regimes can be obtained. These local measurement techniques are first used in a 25.4 mm circular pipe test section. Seven air-water two-phase flow conditions spanning the bubbly, slug, churn-turbulent, and annular flow regimes are measured in this facility. The obtained database contains the radial profiles of both gas- and liquid-phase parameters at three axial locations along the test section. The second facility used in this work contains a 30 mm × 10 mm rectangular test section, in which three two-phase flow and two single-phase flow conditions are measured. Two-dimensional distributions of local two-phase flow parameters in the cross-sectional plane are measured in this facility at three axial locations as well. A facility featuring a 3×3 electrically heated rod bundle is also designed and being constructed in this project. This facility is specially designed for optical measurements and is expected to provide high-quality boiling data in the future. Preliminary analyses have been performed for the data taken in the 25.4 mm circular pipe. Both center-peaked and wall-peaked void fraction profiles have been observed in the data depending on the two-phase flow conditions and/or developing lengths. The 1-D drift-flux model was evaluated with the newly obtained datasets, in which both gas- and liquid-phases data were directly measured. The distribution parameter model has been optimized based on a new void-profile classification method proposed in this study. The optimized drift-flux model shows a significant improvement in predicting both gas velocity and void fraction. The measured liquid-phase turbulence was used to benchmark Sato’s turbulence model considering the bubble-induced shear stress for the three tested bubbly flows. The benchmark results showed good agreement between the PIV measurements and model predictions. In the bubbly flows tested that have low void fractions less than 3%, the effect of the bubble-induced turbulence was found not significant. However, the bubble-induced shear stress becomes important with the increase of the void fraction. The Conjugate Heat Transfer (CHT) model was developed and implemented in NEK-2P. This model allows the coupled simulation of the solid domain and two-phase fluid domain, allowing the specification of realistic boundary conditions. The CHT implementation was verified first with non-boiling simulations. The predicted temperatures in the fluid domain were shown to be identical in simulations with or without the CHT model. The CHT model was then validated through simulations of three Becker benchmark CHF tests performed under both Dryout (DO) and Departure from Nucleate Boiling (DNB) conditions. Reasonably good agreement was obtained between calculated wall temperatures and corresponding experimental data.

42 ENGINEERING↗
DOE OSTI2024

Responses of Marginal and Intrinsic Water-Use Efficiency to Changing Aridity Using FLUXNET Observations

According to classic stomatal optimization theory, plant stomata are regulated to maximize carbon assimilation for a given water loss. A key component of stomatal optimization models is marginal water-use efficiency (mWUE), the ratio of the change of transpiration to the change in carbon assimilation. Although the mWUE is often assumed to be constant, variability of mWUE under changing hydrologic conditions has been reported. However, there has yet to be a consensus on the patterns of mWUE variabilities and their relations with atmospheric aridity. We investigate the dynamics of mWUE in response to vapor pressure deficit (VPD) and aridity index using carbon and water fluxes from 115 eddy covariance towers available from the global database FLUXNET. We demonstrate a non-linear mWUE-VPD relationship at a sub-daily scale in general; mWUE varies substantially at both low and high VPD levels. However, mWUE remains relatively constant within the mid-range of VPD. Despite the highly non-linear relationship between mWUE and VPD, the relationship can be informed by the strong linear relationship between ecosystem-level inherent water-use efficiency (IWUE) and mWUE using the slope, m *. We further identify site-specific m * and its variability with changing site-level aridity across six vegetation types. We suggest accurately representing the relationship between IWUE and VPD using Michaelis–Menten or quadratic functions to ensure precise estimation of mWUE variability for individual sites.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Emergency department visits in California associated with wildfire PM 2.5 : differing risk across individuals and communities

The threats to human health from wildfires and wildfire smoke (WFS) in the United States (US) are increasing due to continued climate change. A growing body of literature has documented important adverse health effects of WFS exposure, but there is insufficient evidence regarding how risk related to WFS exposure varies across individual or community level characteristics. To address this evidence gap, we utilized a large nationwide database of healthcare utilization claims for emergency department (ED) visits in California across multiple wildfire seasons (May through November, 2012–2019) and quantified the health impacts of fine particulate matter <2.5 μm (PM 2.5 ) air pollution attributable to WFS, overall and among subgroups of the population. We aggregated daily counts of ED visits to the level of the Zip Code Tabulation Area (ZCTA) and used a time-stratified case-crossover design and distributed lag non-linear models to estimate the association between WFS and relative risk of ED visits. We further assessed how the association with WFS varied across subgroups defined by age, race, social vulnerability, and residential air conditioning (AC) prevalence. Over a 7 day period, PM 2.5 from WFS was associated with elevated risk of ED visits for all causes (1.04% (0.32%, 1.71%)), non-accidental causes (2.93% (2.16%, 3.70%)), and respiratory disease (15.17% (12.86%, 17.52%)), but not with ED visits for cardiovascular diseases (1.06% (–1.88%, 4.08%)). Analysis across subgroups revealed potential differences in susceptibility by age, race, and AC prevalence, but not across subgroups defined by ZCTA-level Social Vulnerability Index scores. These results suggest that PM 2.5 from WFS is associated with higher rates of all cause, non-accidental, and respiratory ED visits with important heterogeneity across certain subgroups. Notably, lower availability of residential AC was associated with higher health risks related to wildfire activity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

DEEPEN Data Catalog for Magmatic Geothermal Systems in the United States

This data catalog contains information related to the Training Site Analysis for the Geothermica project "DE-risking Exploration of geothermal Plays in magmatic ENvironments (DEEPEN)." The DEEPEN project aims to reduce exploration risk for geothermal fluids in magmatic systems by developing improved an improved framework for interpretation of exploration data using the Play Fairway Analysis (PFA) methodology. The Training Site Analysis performed for DEEPEN leverages existing datasets to develop a customized PFA approach to exploration for multiple geothermal resource types in magmatic systems (conventional hydrothermal resources, supercritical fluid and superheated steam resources, and superhot EGS resources). This data catalog contains links to publicly available data files related to 8 training sites in the United States. US training sites are: the Cascades/Aleutians PFA project; the Hawaii PFA project, the Oregon Cascades PFA project, the Snake River Plain, Idaho PFA project, the Washington State PFA project, Newberry Volcano, Coso Geothermal Field, and the Geysers Geothermal field. This database contains an overview of these training sites, data sources, and links to publicly available exploration datasets. For the five PFA projects, details on exploration data related to PFA components (heat, fluid, permeability, sometimes seal) are provided, including a summary of data weighting methodologies.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

Analysis of Orthogonal Efflux and Permeation Properties of Compounds Leads to the Discovery of New Efflux Pump Inhibitors

Optimization of compound permeation into Gram-negative bacteria is one of the most challenging tasks in the development of antibacterial agents. Two permeability barriers–the passive diffusion barrier of the outer membrane (OM) and active drug efflux–act synergistically to protect cells from the antibacterial action of compounds. In Escherichia coli (E. coli) and relatives, these two barriers sieve compounds based on different physicochemical properties that are defined by their interactions with OM porins and efflux pumps, respectively. In this study, we critically tested the hypothesis that the best substrates and inhibitors of efflux pumps are compounds that can effectively permeate the OM and are available at relatively high concentrations in the periplasm. For this purpose, we filtered a large subset of the ZINC15 database of commercially available compounds for compounds containing a primary amine, a chemical feature known to facilitate the uptake through E. coli general porins. The assembled library was screened by ensemble docking to AcrA, the periplasmic component of the AcrAB-TolC efflux pump, followed by experimental testing of the top predicted binders for antibacterial activities, efflux recognition, and inhibition. In this work, we found that the filtered primary amine library is a rich source of compounds with efflux-inhibiting activities and identified efflux pump inhibitors with novel chemical scaffolds effective against E. coli AcrAB-TolC and efflux pumps of multidrug-resistant clinical isolates of Acinetobacter baumannii. However, primary amines are not required for the recognition of compounds by efflux pumps and their efflux-inhibitory activities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Implications of the correlation between bulge-to-total baryonic mass ratio and the number of satellites for SAGA galaxies

We searched for correlations between the number of satellites and fundamental galactic properties for the Milky Way-like host galaxies in order to better understand their diverse satellite populations. We specifically aim to understand why galaxies that are very similar in stellar mass content, star formation rate, and local environment have very different numbers of satellites. Deep and extensive spectroscopic observations are needed to characterize the complete satellite luminosity function beyond the Local Group. One such endeavor is an ongoing Satellites of Galactic Analogs (SAGA) spectroscopic survey that has completed spectroscopic observations of 36 Milky Way-like galaxies within their virial radii down to the luminosity of Leo I dwarf galaxy. We correlated the number of satellites of SAGA galaxies with several fundamental properties of their hosts – including total specific angular momentum, which is considered to be well preserved throughout galaxy lifetime – in an attempt to identify the main driver of their diverse satellite populations. We aim to reveal some intrinsic galactic property decisive in making more or less satellites irrespective of baryonic mass or the environment in which galaxies reside. We modeled Spitzer Heritage Archive images of SAGA host galaxies at 3.6 and 4.5 microns with GALFIT code to obtain their stellar masses. We also searched the Extragalactic Database for information on their gas content and rotation velocities. Empirical correlations, like the baryonic Tully–Fisher relation and the stellar mass–size relation were used to exclude outliers. All the available galactic properties from the literature along with measured stellar masses were correlated with the number of satellites and no significant correlation was found. However, when we considered the “expected” number of satellites based on the correlation between the baryonic bulge-to-total ratio and the number of satellites confirmed for several nearby galaxies then strong correlations emerge between this number and (1) the mass of the bulge, and (2) the total specific angular momentum. The first correlation is positive, implying that galaxies with more massive bulges have more satellites, as already confirmed. Furthermore, the second correlation with the angular momentum is negative, meaning that, the smaller the angular momentum, the greater the number of expected satellites. This would imply that either satellites cannot form if galaxy angular momentum is too high, or that satellites form inside-out, so that angular momentum is being transferred to the outer parts of the galaxies. However, deeper spectroscopic observations are needed to confirm these findings, because they rely on the expected rather than detected number of satellites. There was a luminosity limit to the SAGA survey equivalent to the luminosity of Leo I dwarf satellite of the Milky Way galaxy (the SAGA limit). In particular, correlations found in this work are very susceptible to the total number of satellites of the NGC 4158 galaxy. This galaxy is predicted to have many more satellites than detected up to the SAGA limit.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Elevating zero dimensional global scaling predictions to self-consistent theory-based simulations

In this work, we have developed an innovative workflow, Stability, Transport, Equilibrium, and Pedestal (STEP)-zero-dimensional (0D), within the OMFIT integrated modeling framework. Through systematic validation against the International Tokamak Physics Activity global H-mode confinement database, we demonstrated that STEP-0D, on average, predicts the energy confinement time with a mean relative error of less than 19%. Moreover, this workflow showed promising potential in predicting plasmas for proposed fusion reactors such as the affordable, robust, compact (ARC) reactor, the European demonstration power plant (EU-DEMO), and the China fusion engineering test reactor (CFETR) indicating moderate H-factors between 0.9 and 1.2. STEP-0D allows theory-based prediction of tokamak scenarios, beginning with 0D quantities. The workflow initiates with the PRO-create module, generating physically consistent plasma profiles and equilibrium using the same 0D quantities as the IPB98(y,2) confinement scaling. This sets the starting point for the STEP module, which further iterates between theory-based physics models of equilibrium, core transport, and pedestal to yield a self-consistent solution. Given these attributes, STEP-0D not only improves the accuracy of predicting plasma performance but also provides a path toward a novel fusion power plant design workflow. When integrated with engineering and costing models within an optimization, this new approach could eliminate the iterative reconciliation between plasma models of varying fidelity. This potential for a more efficient design process underpins STEP-0D's significant contribution to future fusion power plant development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

National Energy Water Treatment & Speciation (NEWTS): A Water & Critical Minerals Database and Dashboard

The poster, presented at the American Geophysical Union (AGU) 2023 Conference, highlights NETL's National Energy Water Treatment & Speciation (NEWTS) Database & Dashboard. This poster reviews the work done to aggregate disparate water quality data for energy-related wastewater streams, to process and integrate the datasets, and enable easy integration with aqueous chemistry modeling software to support water management and beneficial reuse decision-making.

Wenzlick, Madison↗
DOE OSTI2024

AIACHNE's contribution for Nuclear Energy Agency Working Party on International Nuclear Data Evaluation Co-operation Subgroup 50

The AIACHNE (AI/ML Informed cAlifornium CHi Nuclear data Experiment) project aims at designing an experiment for the 252 Cf Prompt Fission Neutron Spectrum (PFNS) that explores systematic biases in an experimental database retrieved from the EXFOR databases. To that end, machine learning (ML) methods were applied to pint-point measurement features likely related to bias. From that information, we selected a feature that should be explored by the AIACHNE experiment. Measurement features are metadata encapsulating all pertinent information about the physical measurement and analysis techniques. Examples are, for instance, what neutron and fission detectors were used for the physical metadata, and what background reduction techniques were employed for analysis techniques. Such metadata were retrieved both from EXFOR entries as well as the literature of data sets described in detail in Reference 2 (at the end of the article).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Intervening alcohol marketing to reduce harmful alcohol use and lessons learned from the theory of changes: Case studies in Thailand

Objectives Globally, the burden of disease caused by alcohol use has been steadily increasing, including in Thailand. In this study, we aim to test the effectiveness of Anderson et al.‘s suggested three approaches to change the collective social norms, which comprise of: (1) providing information and an understanding about alcohol use behaviour, its causes and distribution; (2) focusing strategies on groups rather than individuals; and (3) strengthening supportive laws, regulations and approaches. Study design We employed a mixed-methods approach. Evidence was gathered from literature review and in-depth interviews with key individuals who are responsible for community-based interventions to alcohol marketing strategies in Thailand. Methods We chose to focus on two case studies in Nan and Surin provinces, where hospital-based longitudinal data (8 years) were available. Changes in casualties related to the harmful use of alcohol, resulting from interactions between community-based interventions and alcohol marketing during the time of annual festivals were investigated. We employed the theory of change (ToC) defined by Vogel to guide the data collection and analysis. We reviewed literature from online databases and grey literature to generate causal-loop diagrams. Results We created a causal-loop diagram to describe the complexity of harmful alcohol use, its related factors, context, interventions and outcomes. Over the decade between 2006 and 2015, community-based strategies led to a substantial reduction of casualties (initially a 50% reduction, rising to an 80–90% reduction by the end of the study period) during the time of the festivals. Conclusions The reduction in injuries and fatalities could be a result of the concerted actions, including legal sanctions of alcohol beverage sales and advertisement, and public education to raise awareness and impart knowledge of the harmful use of alcohol. The actions were organised by a coalition of civil society, health professionals, public authorities and community leaders using hospital-based data on the adverse effects of harmful alcohol use to mobilise political support at the provincial level. The availability of long-term financial support as a catalytic source of funds and the presence of a comprehensive alcohol control act enabled framing and mobilisation of local resources and political support.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Survival of Snow in the Melting Layer: Relative Humidity Influence

This study quantifies how far snow can fall into the melting layer (ML) before all snow has melted by examining a combination of in-situ observations from aircraft measurements in Lagrangian spiral descents from above through the ML and descents and ascents into the ML, as well as an extensive database of NOAA surface observer reports during the past 50 years. The airborne data contain information on the particle phase (solid, mixed, or liquid), population size distributions and shapes, along with temperature, relative humidity, and vertical velocity. A wide range of temperatures and ambient relative humidities are used for both the airborne and ground-based data. It is shown that an ice bulb temperature of 0°C, together with the air temperature and pressure (altitude), are good first order predictors of the highest temperature snowflakes can survive in the melting layer before completely melting. Particle size is also important, as is whether the particles are graupel or hail. If the relative humidity is too low, the particles will sublimate completely as they fall into the melting layer. Snow as warm as +7°C is observed from aircraft measurements and surface observations. Snow pellets survive to even warmer temperatures. Relationships are developed to represent the primary findings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Exposing new taxonomic variation with inflammation — a murine model-specific genome database for gut microbiome researchers

The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Novel compound heterozygous CPLANE1 variants identified in a Chinese family with Joubert syndrome

Abstract Joubert syndrome (JS) and JS‐related disorders (JSRD) are a group of neurodevelopmental diseases that share the “molar tooth sign” on axial brain magnetic resonance imaging (MRI), accompanied by cerebellar vermis hypoplasia, ataxia, hypotonia, and developmental delay. To identify variants responsible for the clinical symptoms of a Chinese family with JS and to explore the genotype–phenotype associations, we conducted a series of clinical examinations, including blood tests, brain MRI scans, ultrasound imaging, and ophthalmologic examination. Genomic DNA was extracted from the peripheral blood of the six‐person family, and the pathogenic variants were detected by whole‐exome sequencing (WES) and verified by Sanger sequencing. WES revealed two novel compound heterozygous variants in CPLANE1 : c.1270C>T (p.Arg424*) in exon 10 and c.8901C>A (p.Tyr2967*) in exon 48 of one child, inherited from each parent. Both variants were absent in ethnically matched Chinese control individuals and were either absent or present at very low frequencies in public databases, suggesting that these variants could be the pathogenic triggers of the JS phenotype. Notably, these CPLANE1 sequence variants were related to the pathogenesis of autosomal recessive JS in this study. The newly discovered variants expand the mutation spectrum of CPLANE1 , which assists in understanding the molecular mechanism underlying JS and improving the recognition of genetic counseling, particularly for families with a history of autosomal recessive JS.

Zhang, Cheng↗