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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗
DOE OSTI2021

Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum / Clostridium ljungdahlii Syntrophic Coculture

ABSTRACT Clostridium acetobutylicum and Clostridium ljungdahlii grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate C. ljungdahlii persists in the coculture through proteome exchange during fusing events, which endow C. ljungdahlii cells with expanded substrate utilization, and access to additional reducing equivalents from C. acetobutylicum -evolved H 2 and through acquisition of C. acetobutylicum -native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community. IMPORTANCE Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum / C. ljungdahlii culture is a novel observation that has not been explored in silico . The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify C. ljungdahlii as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Lake Huron Enhances Snowfall Downwind of Lake Erie: A Modeling Study of the 2010 New Year’s Lake Effect Snowfall Event

In the Northeast and Great Lakes regions of the United States, the influence of multiple lakes on the overlying air can greatly affect lake-effect snowfall over downwind communities. To assess the impact of Lake Huron on snowfall downwind of Lake Erie, we simulated a lake-effect snow event which occurred from 1 to 6 January 2010 using the Regional Atmospheric Modeling System (RAMS). We found that the presence of Lake Huron enhances snowfall downwind of Lake Erie by almost 20% and leads to much heavier local snowfall totals than when Lake Huron is not present. This increase in snowfall is due to a lake-to-lake (L2L) convective band, as secondary circulations associated with lake-effect convection form over Lake Huron and persist overland between the lakes before reintensifying over Lake Erie. As these secondary circulations move over Lake Erie, lifting within the upward branch of the circulations accelerates the development of convection within the L2L band. Surface fluxes and convection over Lake Huron deepen the boundary layer, promoting deeper vertical development of this L2L band over Lake Erie. However, although this boundary layer modification strengthens the L2L band, we found that it actually reduced lake-effect snowfall produced by wind-parallel bands (WPB) in other parts of the lake. This indicates that boundary layer modification from upstream lakes may impact L2L bands differently than WPB which are not connected to upstream secondary circulations.

Lake effects↗
DOE OSTI2022

Financial Analysis of Experimental Releases Conducted at Glen Canyon Dam during Water Year 2021

This report was prepared by Argonne National Laboratory (Argonne) in support of a financial analysis of two Glen Canyon Dam (GCD) flow experiments that were conducted in Water Year 2021. The first experiment, called “spring disturbance flow”, was conducted from March 15 to 26, 2021. This disturbance flow experiment is designed to simulate a spring-timed runoff event so scientists can study its effects on the Colorado River ecosystem. The second experiment was a reduced and steady discharge from May 29 to June 4, 2021. This reduced steady flow experiment was conducted for the United States Geological Survey (USGS) to collect high-resolution aerial imagery over Grand Canyon National Park. This analysis was funded by the Colorado River Storage Project (CRSP) Office of the U.S. Department of Energy’s Western Area Power Administration (WAPA). CRSP markets electricity produced by hydroelectric facilities collectively known as the Salt Lake City Area Integrated Projects including dams equipped for power generation on the Colorado, Green, Gunnison, and Rio Grande Rivers and on Plateau Creek in the states of Arizona, Colorado, New Mexico, Utah, and Wyoming. Staff members in Argonne’s Energy Systems Division prepared this technical memorandum with assistance from WAPA’s CRSP and Energy Marketing and Management Offices (EMMO).

58 GEOSCIENCES↗
DOE OSTI2026

Genomic-based biosurveillance for avian influenza: whole genome sequencing from wild mallards sampled during autumn migration in 2022–2023 reveals a high co-infection rate on migration stopover site in Georgia

The Caucasus region, including Georgia, is an important intersection for migratory waterbirds, offering potential for avian influenza virus (AIV) transmission between populations from different geographic areas. In 2022 and 2023, wild ducks were sampled during autumn migration events in Georgia to study the genetic relationships and molecular characteristics of influenza strains. Sequencing and phylogenetic analysis were used to compare the sampled strains to reference sequences from Africa, Asia, and Europe, allowing assessment of genetic relationships and virus transmission between migratory birds. Protein language modeling identified potential co-infections. Of 225 duck samples, 128 tested positive for the influenza M gene. 55 influenza-positive samples underwent whole-genome sequencing, revealing significant diversity. Analysis of the hemagglutinin (HA) segment showed notable differences among subtypes. Most samples were H6N1 and H6N6, but co-infections with combinations like H6H3, N8N1, N6H9, N2N6, and H9H6/N1N2 were also identified. These findings demonstrate the high variability of influenza viruses in migratory waterbirds in Georgia, including a notable rate of co-infections. Some samples exhibited uncommon genetic characteristics compared to other strains from the same year, suggesting Georgia’s role as a mixing vessel for influenza viruses. This facilitates reassortment during co-infections and contributes to the genetic diversity observed across flyways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Machine Learning–Based Approach to Time-series Wave Identification in the Solar Wind

The Wind spacecraft has yielded several decades of high-resolution magnetic field data, a large fraction of which displays small-scale structures. In particular, the solar wind is full of wavelike fluctuations that appear in both the field magnitude and its components. The nature of these fluctuations can be tied to the properties of other structures in the solar wind, such as shocks, that have implications for the time evolution of the solar wind. As such, having a large collection of wave events would facilitate further study of the effects that these fluctuations have on solar wind evolution. Given the large volume of magnetic field data available, machine learning is the most practical approach to classifying the myriad small-scale structures observed. To this end, a subset of Wind data is labeled and used as a training set for a multibranch 1D convolutional neural network aimed at classifying circularly polarized wave modes. Using this algorithm, a preliminary statistical study of 1 yr of data is performed, yielding about 300,000 wave intervals out of about 5,000,000 solar wind intervals. The wave intervals come about more often in the fast solar wind and at higher temperatures, and the number of waves per day is highly periodic. This machine learning–based approach to wave detection has the potential to be a powerful, inexpensive way to catalog waves throughout decades of spacecraft data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Measurement of $\nu_\mu/\bar\nu_\mu$ CC double-differential cross sections on MINERvA hydrocarbon target for the shallow inelastic scattering background region

Cross section measurements are essential for all neutrino oscillation experiments. In fact, uncertaintiesassociated to cross section model parameters constitute one of the dominant sources oferrors in current oscillation analyses. In particular, understanding neutrino-induced pion productionin the kinematic regime known as shallow inelastic scattering (SIS) is critical for improvingneutrino interaction modeling in event generators. In this study, 416,233 (237,468) muon neutrino(antineutrino) interactions are measured in a SIS background region, predominantly made ofbaryon resonances. The analyzed datasets were collected from 2013 to 2019, comprising neutrinosgenerated by the Fermilab NuMI facility, with mean energy of 6 GeV, and the interactions occurredon the MINERvA hydrocarbon target. The measurements are presented as double-differential crosssections in terms of the outgoing muon longitudinal and transverse momentum components, aswell as the Bjorken x and y variables. Comparisons between the extracted data and predictionsfrom several generators reveal significant discrepancies across most kinematic bins.

Souza Correia, Souza Correia, Daniel [Rio de Janei↗
DOE OSTI2021

Learning from many collider events at once

There have been a number of recent proposals to enhance the performance of machine learning strategies for collider physics by combining many distinct events into a single ensemble feature. To evaluate the efficacy of these proposals, we study the connection between single-event classifiers and multievent classifiers under the assumption that collider events are independent and identically distributed. We show how one can build optimal multievent classifiers from single-event classifiers, and we also show how to construct multievent classifiers such that they produce optimal single-event classifiers. This is illustrated for a Gaussian example as well as for classification tasks relevant for searches and measurements at the Large Hadron Collider. We extend our discussion to regression tasks by showing how they can be phrased in terms of parametrized classifiers. Empirically, we find that training a single-event (per-instance) classifier is more effective than training a multievent (per-ensemble) classifier, as least for the cases we studied, and we relate this fact to properties of the loss function gradient in the two cases. While we did not identify a clear benefit from using multievent classifiers in the collider context, we speculate on the potential value of these methods in cases involving only approximate independence, as relevant for jet substructure studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

A broad-host-range event detector: expanding and quantifying performance between Escherichia coli and Pseudomonas species

Modern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli . It is clear that new applications such as chemical sensing and event logging in complex environments will benefit from new host chassis. This study quantitatively compared how the same chemical event logger performed across four strains and three different microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads— Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two benchmark E. coli chassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and downstream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Wintertime extreme warming events in the high Arctic: characteristics, drivers, trends, and the role of atmospheric rivers

Abstract. An extreme warming event near the North Pole, with 2 m temperature rising above 0 °C, was observed in late December 2015. This specific event has been attributed to cyclones and their associated moisture intrusions. However, little is known about the characteristics and drivers of similar events in the historical record. Here, using data from European Centre for Medium-Range Weather Forecasts Reanalysis, version 5 (ERA5), we study these winter extreme warming events with 2 m temperature over a grid point above 0 °C over the high Arctic (poleward of 80° N) that occurred during 1980–2021. In ERA5, such wintertime extreme warming events can only be found over the Atlantic sector. They occur rarely over many grid points, with a total absence during some winters. Furthermore, even when occurring, they tend to be short-lived, with the majority of the events lasting for less than a day. By examining their surface energy budget, we found that these events transition with increasing latitude from a regime dominated by turbulent heat flux into the one dominated by downward longwave radiation. Positive sea level pressure anomalies which resemble blocking over northern Eurasia are identified as a key ingredient in driving these events, as they can effectively deflect the eastward propagating cyclones poleward, leading to intense moisture and heat intrusions into the high Arctic. Using an atmospheric river (AR) detection algorithm, the roles of ARs in contributing to the occurrence of these extreme warming events defined at the grid-point scale are explicitly quantified. The importance of ARs in inducing these events increases with latitude. Poleward of about 83° N, 100 % of these events occurred under AR conditions, corroborating that ARs were essential in contributing to the occurrence of these events. Over the past 4 decades, both the frequency, duration, and magnitude of these events have been increasing significantly. As the Arctic continues to warm, these events are likely to increase in both frequency, duration, and magnitude, with great implications for the local sea ice, hydrological cycle, and ecosystem.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Exploratory Efforts to Constrain Geologic Material Properties from Remote Sensing Data: A Joint Study

Identification and characterization of underground events from surface or remote data requires a thorough understanding of the rock material properties. However, material properties usually come from borehole data, which is expensive and not always available. A potential alternative is to use topographic characteristics to approximate the strength, but this has never been done before quantitatively. Here we present the results from the first steps towards this goal. We have found that there are strong correlations between compressive and tensile strengths and slopes, but these correlations vary depending on data analysis details. Rugosity may be better correlated to strength than slope values. More comprehensive analyses are needed to fully understand the best method of predicting strength from topography for this area. We also found that misalignment of multiple GIS datasets can have a large influence on the ability to make interpretations. Lastly, these results will require further study in a variety of climatic conditions before being applicable to other sites.

42 ENGINEERING↗
DOE OSTI2019

Aftershock deficiency of induced earthquake sequences during rapid mitigation efforts in Oklahoma

Induced seismicity provides a rare opportunity to study earthquake triggering and underlying stress perturbations. Triggering can be a direct result of induced stress changes or indirect due to elastic stress transfer from preceding events leading to aftershocks. Both of these processes are observable in areas with larger magnitude induced events, such as Oklahoma. We study aftershock sequences of M2.5 to M5.8 earthquakes and examine the impact of targeted injection rate reductions. In comparing aftershock productivity between California and Oklahoma, we find similar exponential scaling statistics between mainshock magnitude and average number of aftershocks. For events with M≥4.5 Oklahoma exhibits several mainshocks with total number of aftershocks significantly below the average scaling behavior. The sequences with deficient aftershock numbers also experienced rapid, strong mitigation and reduced injection rates, whereas two events with M4.8 and M5.0 with weak mitigation exhibit normal aftershock productivity. The timing of when aftershock activity is reduced correlates with drops in injection rates with a lag time of several days. Large mainshocks with significantly reduced aftershocks may explain decreasing seismicity rates while seismic moment release was still increasing in Oklahoma in 2016. We investigate the expected poroelastic stress perturbations due to injection rate changes within a layered axisymmetric model and find that stresses are lowered by 10s to 100s kPa within the injection-affected zone. For earthquakes induced by poroelastic stress-increase at several kilometers from wells, the rapid shut-in of wells may lead to elastic stress reductions sufficiently high to arrest unfolding aftershock sequences within days after mitigation starts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Evaluating Extreme Storm Events in an Ensemble of High‐Resolution Projections

This study uses different downscaling techniques and reference observations to investigate the characteristics of extreme storm events over the conterminous United States in historical and a projected future scenario. While previous studies agree on the projected changes in intensity and frequency of precipitation extremes, there is a lack of consensus regarding how their size will change in response to an increase in radiative forcing. Moreover, the influence of different downscaling techniques on their characteristics has not been thoroughly examined. This study employs an ensemble of high‐resolution projections derived from six CMIP6 GCMs, using dynamical, statistical and artificial intelligence based downscaling techniques and two reference observations. Overall, we find noticeable differences in the size, average depth, and total precipitation volume of these storms among the climate ensembles in the historical period. Despite these differences in the historical period, we find consistent future changes across various ensembles. We find a robust projected increase in storm size during Winter and Spring but a decrease in size during Summer in the East. Nevertheless, irrespective of changes in their size, extreme storms are projected to intensify across all the ensembles and seasons.

Rastogi, Deeksha [Oak Ridge National Laboratory (O↗
DOE OSTI2026

How Frequent Will the Rarest Daily Rainfall Records of Hurricane Ida’s Remnants Be in the Future?

Abstract Gaining continued insights into the impact of global warming on the occurrence of hurricane-associated intense record downpours is essential for building climate resilient communities. This study investigates projected future changes in extreme rainfall over the Northeast United States, as represented by extreme daily amounts during Hurricane Ida in 2021. We used historical control simulations of Weather Research and Forecasting (WRF) Model generated from 40 years of weather events (1980–2014, 12 km) forced by the fifth generation European Centre for Medium-Range Weather Forecasts atmospheric reanalysis. These simulations are thermodynamically modified (2060–2100) via an imposed warming for the high-emission scenario of shared socioeconomic pathway (SSP585) from a range of general circulation models. Ground observations from the Global Historical Climatology Network (1950–2014) and WRF simulations (historical, 1980–2014, and future, 2060–2100) are integrated into a nonstationary generalized extreme value (GEV) framework to assess the frequency of Ida’s heaviest daily rain rates under the SSP585 scenario. Results show that Ida’s daily maximum rainfall recorded at different observation locations was higher than the single highest September daily maximum observed (1950–2014) for 5 out of 17 stations (∼30% of the stations). Ida-like extreme daily rain rates are projected to be, on average, more than 2 times more likely to occur at the end of the century in the simulations (with some regions as high as 5 times). This work demonstrates that integrating a high-resolution atmospheric model’s present-day and thermodynamically modified future simulations along with ground observations, within a nonstationary statistical framework, is crucial for understanding changing characteristics of extreme weather events. Significance Statement Daily scale extreme precipitation is expected to become more frequent and severe, as evidenced by observations and model simulations. While it is important to investigate how these intensifying heavy rainfall events affect current engineering standards, fewer studies have contextualized how warming impacts the most extreme rainfall from a single storm event relative to historical heavy downpours. In this study, we focused on the daily extreme rainfall associated with the extratropical transition of Hurricane Ida (2021), particularly over the northeastern United States—some of which exceeded the commonly used hydrologic design criteria for a 100-yr storm. Using a high-resolution atmospheric model simulation, we investigated how continued warming may influence the frequency of such daily rain rates. Under a high-emission scenario, these events are projected to become up to 5 times more likely at the end of the twenty-first century.

Dollan, Ishrat J↗
DOE OSTI2021

Legacy effects of drought on tree growth responses to hurricanes

Natural perturbations, including hurricanes and severe droughts, are becoming more frequent and intense in the tropics, yet our understanding of forest responses to these events is still limited. While the relationships between extreme climatic events and tree mortality are frequently studied, responses of trees that survived such perturbations have been rarely reported. Perturbations and their effects can be quite variable, and trees can respond both positively and negatively to them, depending on their sensitivity and opportunistic behavior. Understanding the potential variation in responses both within and among species is important for building predictions of forest responses. We studied tree growth responses (i.e., changes relative to standard conditions) to hurricanes and drought events in Puerto Rico across six common and broadly distributed species. We examined whether there is a congruence in responses to these contrasting extreme climatic events. We show that trees are particularly susceptible to droughts but display a wide range of responses to hurricanes. Despite the high stochasticity in the impacts of hurricanes, trees that showed reduced growth during previous droughts tend to show reduced growth during the hurricanes as well. Our results demonstrate that trees subjected to different and successive major climatic stresses have consistent declines in their performance. Projected increases in the severity of droughts and tropical storms could have an accumulated, and possibly compound, impact on tree growth. Long-term demographic studies are necessary to understand legacy effects of species responses to extreme climatic perturbations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Synchrophasor Measurements-based Events Detection Using Deep Learning

Deep learning algorithms have been developed for phasor measurement units (PMUs) analysis aiming at providing grid operators to observe and react to significant real-time changes in the grid associated with multiple factors (e.g., power generation and load variations, different type of faults, and equipment mailfunction), or for offline post-event system diagnostics. In this study, a Long Short-Term Memory (LSTM)-based deep neural network (DNN) is adopted and evaluated to identify the most appropriate model configurations for event detection and longer-term anomalous pattern extraction. The proposed DNN model shows the potential on long-term predictions with the ability to capture nonlinear and nonstationary mixture complex patterns in PMU datasets. Real-world PMU in the WECC system were used for model development and validation.

deep learning↗
DOE OSTI2025

Path Sampling for Rare Events Boosted by Machine Learning

The study by Jung et al. introduced Artificial Intelligence for Molecular Mechanism Discovery (AIMMD), a novel sampling algorithm that integrates machine learning to enhance the efficiency of transition path sampling (TPS). By enabling on-the-fly estimation of the committor probability and simultaneously deriving a human-interpretable reaction coordinate, AIMMD offers a robust framework for elucidating the mechanistic pathways of complex molecular processes. Here, this commentary provides a discussion and critical analysis of the core AIMMD framework, explores its recent extensions, and offers an assessment of the method’s potential impact and limitations.

Minh, Porhouy [Univ. of Minnesota, Minneapolis, MN↗