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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Apple Bitter Rot: Biology, Ecology, Omics, Virulence Factors, and Management of Causal Colletotrichum Species

ABSTRACT Apple bitter rot is caused by various Colletotrichum spp. that threaten apple production globally resulting in millions of dollars in damage annually. The fungus causes a decline in fruit quality and yield, eventually rotting the fruit and rendering it inedible. The pathogen is difficult to keep out of orchards because of its broad host range and transmissibility by rain splash and insects. Once the disease manifests, pathogen identification is difficult due to evolving taxonomy and similar morphology between species. Current management strategies are threatened by an increase in fungicide resistance and regulations on many multisite fungicides, leading to a pressing need for new management options for control. This review aims to summarise the most current knowledge regarding the biology, virulence factors, ecology, omics and emerging management strategies for Colletotrichum species that cause apple bitter rot. Taxonomy Colletotrichum species—Domain Eukaryota, Kingdom Fungi, Phylum Ascomycota, Class Sordariomycetes, Order Glomerellales, Family Glomerellaceae, Genus Colletotrichum . Biology Hemibiotrophic pathogen with a wide host range that establishes a biotrophic interaction where it penetrates host plants using appressoria followed by a switch to necrotrophy causing rot symptoms. Toxins Cercosporin, colletotrichins, colletotric acid, ferricrocin. Host Range The host range varies by species but largely occurs on dicotyledonous plants and is less prevalent on monocots as well as gymnosperms, ferns, mosses and animals (e.g., insects). Disease Symptoms Symptoms often manifest as flat to sunken necrotic areas on fruit. Lesions on leaves and fruit can have concentric rings with abundant pathogen sporulation. Disease Control Colletotrichum spp. are primarily managed by single‐site quinone outside inhibitor (Qol), methyl benzimidazole carbamate (MBC), demethylation inhibitor (DMI) fungicides, and multisite dithiocarbamate and phthalimide fungicides. Susceptibility may vary with species, strain specificity, or geographic region. Other management options include clean stock production, cultural practices, resistance breeding, and biological control through the introduction of protective or competing microorganisms.

Boeckman, Nathanial J. [Plant Pathology Laboratory↗
DOE OSTI2025

Pine‐fungal co‐invasion alters whole‐ecosystem properties of a native eucalypt forest

Summary Pine‐fungal co‐invasions into native ecosystems are increasingly prevalent across the southern hemisphere. In Australia, invasive pines slowly spread into native eucalypt forests, creating novel mixed forests. We sought to understand how pine‐fungal co‐invasions impact interconnected above‐ and belowground ecosystem characteristics. We sampled beneath maturePinus radiataandEucalyptus racemosain a pine‐invaded eucalypt forest in New South Wales, Australia. We measured microbial community composition via amplicon sequencing of 16S, ITS2, and 18S rDNA regions, microbial metabolic activity via Biolog plate substrate utilization, and soil, leaf litter, and understory plant characteristics. Pines were associated with decreased topsoil moisture, increased pine litter, and decreased eucalypt litter total phosphorus content. Soils and roots beneath pines had distinct microbial community composition and activity relative to eucalypts, including decreased bacterial diversity, decreased microbial utilization of several C‐ and N‐rich substrates, and enrichment of pine‐associated ectomycorrhizae. Introduced suilloid fungi were abundant across both pine and eucalypt soils and roots. Many ecosystem impacts increased with pine size. Invasive pines and their ectomycorrhizae have significant impacts on eucalypt forest properties as they grow. Interconnected impacts at the scale of individual trees should be considered when managing invaded forests and predicting effects of pine invasions.

Plant Sciences↗
DOE OSTI2025

Populus PtrbHLH011 Is a Transcriptional Co‐Regulator Involved in the Activation of Cell Wall Biosynthesis by Iron Deprivation

The lack of a mechanistic understanding of the environmental plasticity of secondary cell wall (SCW) biosynthesis restricts large-scale biomass and bioenergy production on marginal lands. Using Populus (poplar), a key bioenergy crop, we discovered that iron deprivation, a prevalent abiotic stress on marginal lands, stimulates SCW biosynthesis in stems. We identified the transcription factor PtrbHLH011 as a critical regulator underlying this response. Through integrated analyses involving phenotypic characterisation of PtrbHLH011 knockout and overexpression plants, functional genomics and molecular investigations, we established that PtrbHLH011 functions as a central regulator of SCW biosynthesis, iron homeostasis and flavonoid biosynthesis by directly repressing essential genes in these pathways. Iron deprivation downregulates PtrbHLH011 expression, subsequently activating these biosynthetic pathways. Notably, cytosine base editing-based knockout of PtrbHLH011 significantly enhanced plant growth, yielding up to a 110% increase in stem diameter and a 300% increase in leaf iron content. These findings present a novel regulatory mechanism linking environmental iron availability to SCW biosynthesis and illustrate a practical strategy to improve biomass yield on iron-deficient marginal lands. Furthermore, our mechanistic insights into PtrbHLH011 target recognition and regulation provide a valuable foundation for precise manipulation of gene regulatory networks, facilitating the development of high-performance bioenergy crops adapted to marginal environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity

SUMMARY Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum ( Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high‐density genomic marker set of 43 983 694 variants including single‐nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower‐density marker sets. WGS identified and scored variants in 5‐kb bins where available genotyping‐by‐sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six F st peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fracture Sustainability in Enhanced Geothermal Systems: Experimental and Modeling Constraints

Enhanced geothermal systems (EGS) offer the potential for a much larger energy source than conventional hydrothermal systems. Hot, low-permeability rocks are prevalent at depth around the world, but the challenge of extracting thermal energy depends on the ability to create and sustain open fracture networks. Laboratory experiments were conducted using a suite of selected rock cores (granite, metasediment, rhyolite ash-flow tuff, and silicified rhyolitic tuff) at relevant pressures (uniaxial loading up to 20.7 MPa and fluid pressures up to 10.3 MPa) and temperatures (150–250 °C) to evaluate the potential impacts of circulating fluids through fractured rock by monitoring changes in fracture aperture, mineralogy, permeability, and fluid chemistry. Because a fluid in disequilibrium with the rocks (deionized water) was used for these experiments, there was net dissolution of the rock sample: this increased with increasing temperature and experiment duration. Thermal-hydrological-mechanical-chemical (THMC) modeling simulations were performed for the rhyolite ash-flow tuff experiment to test the ability to predict the observed changes. These simulations were performed in two steps: a thermal-hydrological-mechanical (THM) simulation to evaluate the effects of compression of the fracture, and a thermal-hydrological-chemical (THC) simulation to evaluate the effects of hydrothermal reactions on the fracture mineralogy, porosity, and permeability. Furthermore, these experiments and simulations point out how differences in rock mineralogy, fluid chemistry, and geomechanical properties influence how long asperity-propped fracture apertures may be sustained. Such core-scale experiments and simulations can be used to predict EGS reservoir behavior on the field scale.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Measurement of Deformation Heterogeneity During Shale Swelling Using Digital Image Correlation

Abstract Rock-fluid interactions in shale formations are one of the main sources of wellbore instability issues and inadequate stimulation performance. For better planning of fracturing operations and optimizing production from these reservoirs, it is important to understand the mechanisms behind these interactions. These issues are especially prevalent in clay-rich shales, such as Tuscaloosa Marine Shale, which is the subject of this study. Conventional techniques to quantify these shale-fluid interactions comprise of measuring swelling in powdered rock grains or measurement of deformation in the whole pieces of the core using a linear variable differential transformer and strain gages. However, the contribution from individual laminae to overall deformation cannot be evaluated using these methods. In this study, we developed an experimental setup to evaluate the spatial deformation in shale during interaction with water using digital image correlation (DIC). Deformation of two shale samples, with 34 wt% to 51 wt% clay content, was studied. White paint was used to generate a random speckle pattern on the specimen and then immersed in deionized water. The deformation process was captured using a digital camera and images were analyzed using DIC to quantify the deformation. The implementation of the DIC technique enables the visualization and quantification of spatial deformation in the specimen during interacting with water. The results show the localization of large strains in select laminations. The results provide a better understanding of shale deformation when interacting with water in comparison to traditional measurements that can provide only an average strain value.

Energy & Fuels↗
DOE OSTI2022

Computational Elucidation of Mechanical Degradation in NMC Cathodes: Impact on Cell Performance

Next-generation lithium ion batteries are expected to demonstrate superior energy and power density with longer cycle life for successful electrification of the automobile, aviation, and marine industries. Adoption of lithium metal anodes with solid electrolytes can help to achieve that goal given that the dendrite-related issues are solved eventually. Another possibility is to use Ni-rich high-capacity NMC cathode materials with liquid and/or solid electrolytes, which presently experiences rapid capacity fade while charged to higher voltages. Several mechanical and chemical degradation mechanisms are active within these NMC-based cathode particles. Recent experimental research activities attempted to correlate the mechanical damage with the capacity fade experienced by Ni-rich LiNi x Mn y Co z O 2 (x+y+z = 1) (NMC) cathodes. Here, a computational framework is developed in this study capable of quantifying the evolution of inter primary particle and cathode/electrolyte interfacial fracture experienced by the poly- and single-crystalline NMC cathodes during charge/discharge operation. Influences of mechanical degradation on the overall cell capacity, while operating with liquid and/or solid electrolytes, are successfully characterized. Decreasing the size of the cathode primary particles, or the size of the single-crystalline cathodes, can mitigate the overall mechanical degradation, and subsequent capacity fade, experienced by NMC cathodes. The developed theoretical methodology can help the engineers and scientists to better understand the mechanical degradation mechanism prevalent in Ni-rich NMC cathodes and build superior lithium ion-based energy storage devices for the application in next-generation devices.

25 ENERGY STORAGE↗
DOE OSTI2023

Direct Numerical Simulation of Partial Fuel Stratification Assisted Lean Premixed Combustion for Assessment of Hybrid G-Equation/Well-Stirred Reactor Model

Partial fuel stratification (PFS) is a promising fuel injection strategy to stabilize lean premixed combustion in spark-ignition (SI) engines. PFS creates a locally stratified mixture by injecting a fraction of the fuel, just before spark timing, into the engine cylinder containing homogeneous lean fuel/air mixture. Further, this locally stratified mixture, when ignited, results in complex flame structure and propagation modes similar to partially premixed flames and allows for faster and more stable flame propagation than a homogeneous lean mixture. This study focuses on understanding the detailed flame structures associated with PFS-assisted lean premixed combustion. First, a two-dimensional direct numerical simulation (DNS) is performed using detailed fuel chemistry, experimental pressure trace, and realistic initial conditions mapped from a prior engine large-eddy simulation (LES), replicating practical lean SI operating conditions. DNS results suggest that the conventional triple flame structure is prevalent during the initial stage of flame kernel growth. Both premixed and nonpremixed combustion modes are present with the premixed mode contributing dominantly to the total heat release. Detailed analysis further reveals the effects of flame stretch and fuel pyrolysis on flame displacement speed. Based on the DNS findings, the accuracy of a hybrid G-equation/well-stirred reactor (WSR) combustion model is assessed for the PFS-assisted lean operation in the LES context. It is found that the G-equation model qualitatively captures the premixed branches of the triple flame, while the WSR model predicts the nonpremixed branch of the triple flame. Finally, potential needs for improvements to the hybrid G-equation/WSR modeling approach are discussed.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2022

Image transformers for classifying acute lymphoblastic leukemia

Cancer is the leading cause of death by disease in American children. Each year, nearly 16,000 children in the United States and over 300,000 children globally are diagnosed with cancer. Leukemia is a form of blood cancer that originates in the bone marrow and accounts for one-third of pediatric cancers. This disease occurs when the bone marrow contains 20% or more immature white blood cell blasts. Acute lymphoblastic leukemia is the most prevalent leukemia type found in children, with half of all annual cases in the U.S. diagnosed for subjects under 20 years of age. To diagnose acute lymphoblastic leukemia, pathologists often conduct a morphological bone marrow assessment. This assessment determines whether the immature white blood cell blasts in bone marrow display the correct morphological characteristics, such as size and appearance of nuclei. Pathologists also use immunophenotyping via multi-channel flow cytometry to test whether certain antigens are present on the surface of blast cells; the antigens are used to identify the cell lineage of acute lymphoblastic leukemia. These manual processes require well-trained personnel and medical professionals, thus being costly in time and expenses. Computerized decision support via machine learning can accelerate the diagnosis process and reduce the cost. Training a reliable classification model to distinguish between mature and immature white blood cells is essential to the decision support system. Here, we adopted the Vision Transformer model to classify white blood cells. The Vision Transformer achieved superb classification performance compared to state-of-the-art convolutional neural networks while requiring less computational resources for training. Additionally, the latent self-attention architecture provided attention maps for a given image, providing clues as to which portion(s) of the image were significant in decision-making. We applied the Vision Transformer model and a convolutional neural network model to an acute lymphoblastic leukemia classification dataset of 12,528 samples and achieved accuracies of 88.4% and 86.2%.

Cho, Priscilla↗
DOE OSTI2022

Reducing opioid use disorder and overdose deaths in the United States: A dynamic modeling analysis

Opioid overdose deaths remain a major public health crisis. We used a system dynamics simulation model of the U.S. opioid-using population age 12 and older to explore the impacts of 11 strategies on the prevalence of opioid use disorder (OUD) and fatal opioid overdoses from 2022 to 2032. These strategies spanned opioid misuse and OUD prevention, buprenorphine capacity, recovery support, and overdose harm reduction. By 2032, three strategies saved the most lives: (i) reducing the risk of opioid overdose involving fentanyl use, which may be achieved through fentanyl-focused harm reduction services; (ii) increasing naloxone distribution to people who use opioids; and (iii) recovery support for people in remission, which reduced deaths by reducing OUD. Increasing buprenorphine providers’ capacity to treat more people decreased fatal overdose, but only in the short term. Our analysis provides insight into the kinds of multifaceted approaches needed to save lives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Dependence of tropical cyclone seeds and climate sensitivity on tropical cloud response

Projections of future tropical cyclone frequency are uncertain, ranging from a slight increase to a considerable decrease according to climate models. Estimation of how much the Earth’s surface temperature warms in response to greenhouse gas increase, quantified by effective climate sensitivity, is also uncertain. These two uncertainties have historically been studied independently as they concern different scales: One quantifies the extreme weather and the other the mean climate. Here, we show that these two uncertainties are not independent and are both influenced by the response of tropical clouds to warming. Across climate models, we show an anticorrelation between shortwave cloud radiative feedback and changes in the frequency of seed vortices, a prevalent type of tropical cyclone precursors. We further show an anticorrelation between effective climate sensitivity and tropical cyclone frequency changes, suggesting that global tropical cyclone frequency tends to decrease more substantially in models with larger temperature increase.

Science & Technology - Other Topics↗
DOE OSTI2023

Alkylperoxy radicals are responsible for the formation of oxygenated primary organic aerosol

Organic aerosol (OA) is an air pollutant ubiquitous in urban atmospheres. Urban OA is usually apportioned into primary OA (POA), mostly emitted by mobile sources, and secondary OA (SOA), which forms in the atmosphere due to oxidation of gas-phase precursors from anthropogenic and biogenic sources. By performing coordinated measurements in the particle phase and the gas phase, we show that the alkylperoxy radical chemistry that is responsible for low-temperature ignition also leads to the formation of oxygenated POA (OxyPOA). OxyPOA is distinct from POA emitted during high-temperature ignition and is chemically similar to SOA. We present evidence for the prevalence of OxyPOA in emissions of a spark-ignition engine and a next-generation advanced compression-ignition engine, highlighting the importance of understanding OxyPOA for predicting urban air pollution patterns in current and future atmospheres.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Coherent charge hopping suppresses photoexcited small polarons in ErFeO 3 by antiadiabatic formation mechanism

Polarons are prevalent in condensed matter systems with strong electron-phonon coupling. The adiabaticity of the polaron relates to its transport properties and spatial extent. To date, only adiabatic small polaron formation has been measured following photoexcitation. The lattice reorganization energy is large enough that the first electron–optical phonon scattering event creates a small polaron without requiring substantial carrier thermalization. We measure that frustrating the iron-centered octahedra in the rare-earth orthoferrite ErFeO 3 leads to antiadiabatic polaron formation. Coherent charge hopping between neighboring Fe 3+ –Fe 2+ sites is measured with transient extreme ultraviolet spectroscopy and lasts several picoseconds before the polaron forms. The resulting small polaron formation time is an order of magnitude longer than previous measurements and indicates a shallow potential well, even in the excited state. The results emphasize the importance of considering dynamic electron-electron correlations, not just electron-phonon–induced lattice changes, for small polarons for transport, catalysis, and photoexcited applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Ab initio investigation of a hypersonic double cone experiment

This article presents a direct molecular simulation (DMS) of a reactive Mach 8.2 oxygen flow over a double cone geometry. The free stream conditions and article configuration generate a flow with thermal and chemical nonequilibrium, which are common attributes of hypersonic flight. This scenario was first studied experimentally at Calspan University of Buffalo Research Center’s test facility. DMS is a particle method that uses quantum mechanically derived interaction potentials to simulate molecular collisions within a flow field. Since these interaction potentials are the only modeling inputs used in the simulation, all flow features can solely be attributed to the ab initio potential energy surfaces. Hence, providing a comparison of a hypersonic ground test and numerical data anchored to quantum mechanics. The fundamental nature of DMS is leveraged to investigate molecular level mechanisms prevalent in the flow, and comparisons with lower fidelity simulations are presented to highlight the role of these first principles calculations as benchmark solutions.

Science & Technology - Other Topics↗
DOE OSTI2025

Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance

For over two decades, artemisinin-based combination therapy (ACT) has been the standard of care for the treatment of uncomplicated falciparum malaria. However, artemisinin partial resistance (ART-R) is now prevalent in Southeast Asia and has emerged in eastern Africa, threatening ACT efficacy. Artefenomel, a synthetic 1,2,4-trioxolane, exhibits an extended pharmacokinetic exposure profile that predicts for efficacy against ART-R parasites. Unfortunately, the development of artefenomel was halted recently after almost a decade in the clinic. Here, we describe studies of an artefenomel-adjacent chemotype that combines potent in vitro activity against clinical ART-R parasites, an extended pharmacokinetic profile with single-exposure efficacy in a murine malaria model, and enhanced stability in human microsomes and hepatocytes. Overall, our studies reveal a heretofore underexplored trioxolane chemotype with the potential to address ART-R in a next-generation trioxolane development candidate.

Science & Technology - Other Topics↗
DOE OSTI2025

Extending tetrahedral network similarity to carbon: A type-I carbon clathrate stabilized by boron

Clathrates are guest/host framework compounds composed of polyhedral cages, yet despite their prevalence among tetrahedral network formers, clathrates with a carbon host lattice remain unrealized synthetic targets. Here, we report a type-I carbon-based framework—a ubiquitous clathrate structure type found throughout compounds containing tetrahedral building blocks. Following a boron-stabilization scheme based on first-principles predictions in the Ca–B–C system at high pressure, type-I Ca 8 B x C 46−x (x ≈ 9) was synthesized in the archetypal $Pm\bar{3}n$ lattice with stability derived from substitutionally disordered boron atoms on hexagonal ring framework positions. The synthesized clathrate, which is recoverable to ambient conditions, expands topological network similarity across tetrahedral systems and opens possibilities for a broad family of diamond-like, carbon-based compounds with tunable properties based on the wide potential for guest/host-atom substitutions and framework versatility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

As above, not so below: Ion fractionation in planetary analog ices

The geophysical evolution and astrobiological potential of ocean worlds are indelibly linked to the chemical compositions of their oceans and ice shells. In the absence of direct measurements, empirical estimates of subsurface ocean compositions have relied on the assumption that the ionic compositions of ice shell surfaces are representative of their underlying ocean compositions. Here, we present experimental results demonstrating that ion fractionation—the differential entrainment of ion species in forming ices—is likely a prevalent process on ocean worlds, suggesting that planetary ice shell compositions do not directly reflect their underlying ocean compositions. We measure in-ice depletions and amplifications of relative ion concentrations ranging between −40 and +77%, compared to the parent fluid composition. Although this may complicate the interpretation of spacecraft data, ion fractionation provides a mechanism for generating compositionally diverse ices that could help explain the geological complexity of planetary ice shells.

58 GEOSCIENCES↗
DOE OSTI2026

Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism

Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.

Chen, LinXing [University of Science and Technolog↗