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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Müllerian mimicry and the coloration patterns of sympatric coral snakes

Abstract Coral snakes in the genus Micrurus are venomous, aposematic organisms that signal danger to predators through vivid coloration. Previous studies found that they serve as models to several harmless species of Batesian mimics. However, the extent to which Micrurus species engage in Müllerian mimicry remains poorly understood. We integrate detailed morphological and geographical distribution data to investigate if coral snakes are Müllerian mimics. We found that coloration is spatially structured and that Micrurus species tend to be more similar where they co-occur. Though long supposed, we demonstrate for the first time that coral snakes might indeed be Müllerian mimics as they show some convergence in coloration patterns. Additionally, we found that the length of red-coloured rings in Micrurus is conserved, even at large geographic scales. This finding suggests that bright red rings may be under more substantial stabilizing selection than other aspects of coloration and probably function as a generalized signal for deterring predators.

Evolutionary Biology↗

DOE OSTI2021

Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi

ABSTRACT Bacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Transcription Factors Controlling the Rhizobium–Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment

Abstract Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium–legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium–legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium–legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium–legume symbiosis.

Cell Biology↗

DOE OSTI2022

Frontiers and opportunities in bioenergy crop microbiome research networks

Researchers from across the four U.S. Department of Energy Bioenergy Research Centers engaged in a microbiome workshop that focused on identifying challenges and collaboration opportunities to better understand bioenergy-relevant plant–microbe interactions. The virtual workshop included hands-on educational sessions and a keynote address on current best practices in microbiome science and community microbiome standards, as well as breakout sessions aimed at identifying microbiome-related data and measurements that should be prioritized, opportunities for and barriers to integrating plant metabolites to microbiome research, and strategies for more effectively integrating microbiome data and processes into existing models. Based on participant discussion, key findings of the workshop were the need to prioritize scaling data sharing across BRCs and the broader research community and securing collaborative infrastructure in the areas of microbiome-ecosystem modeling and molecular plant-microbe interactions. This workshop review highlights additional main findings from this event, to encourage cross-site and more holistic meta-analyses while promoting wide scientific community engagement across plant microbiome sciences.

09 BIOMASS FUELS↗

DOE OSTI2022

Self-Protective Inverters Against Malicious Setpoints Using Analytical Reference Models

This paper presents the concept of self-protective inverters using reference models. In the proposed method, incoming setpoints from the utility operator or third-party aggregators are inspected using analytical reference models before engaging the setpoints to the inverter’s local controller. When a malicious setpoint passes the existing security layers, a smart inverter can examine the integrity of an incoming setpoint in real-time. The efficacy of the developed method has been tested using a laboratory setup, including a three-phase 3kVA SiC-MOSFET inverter and a 12kW NHR 9410 regenerative grid emulator. Furthermore, the results verify that the developed analytical models can provide device-level protection for grid-interactive inverters by inspecting and preventing harmful setpoints from getting engaged to the local controller.

42 ENGINEERING↗

DOE OSTI2021

A regional inter-disciplinary partnership focusing on the development of a carinata-centered bioeconomy

Brassica carinata or Ethiopian mustard, a non-edible oilseed brassica, is a low carbon, purpose-grown, and none-to-low indirect land-use change bioenergy feedstock for the production of drop-in sustainable aviation fuel, biodiesel, renewable diesel, and a suite of value-added coproducts. Carinata oil converted to drop-in fuel using an American Society for Testing and Materials approved Catalytic Hydrothermolysis process has been successfully tested in commercial and military aviation. Carinata meal, the residue after oil extraction, is a high-protein feed supplement for livestock, poultry, and swine, and can also yield specialty products. The Southeast Partnership for Advanced Renewables from Carinata (SPARC) is a public–private partnership formed with a twofold mission: (1) Removing physical, environmental, social, and economic constraints that prevent regional intensification of carinata production as a low-carbon feedstock for renewable fuel and coproducts and (2) demonstrating enhanced value across the entire value chain by mitigating risk to farmers and other stakeholders. The partnership's goal is to energize the US bioeconomy through sustainable agriculture and thus contribute to energy security and economic diversification. SPARC relies on a combination of cutting-edge multidisciplinary research and active industry engagement to facilitate adoption of the crop. This involves informing stakeholders along the entire supply chain, from producers to end-users, policymakers, influencers, and the public, about the opportunities and best practices related to carinata. This article provides context and background concerning carinata commercialization as a winter cash crop in the Southeast US for renewable fuels and bioproducts. The advances made to date in the areas of feedstock development, fuel and coproduct development, meal valorization, supply chain logistics, and stakeholder engagement are outlined.

09 BIOMASS FUELS↗

DOE OSTI2025

UrbanScaping: Community Spatial Data Visualization & Analytics

Evaluating the electrification potential of buildings through retrofitting is crucial for reducing carbon emissions and the carbon footprint of built environments. This study leverages the Automatic Building Energy Modeling (AutoBEM) software, integrating the Model America database to create an urban context-based spatial analysis platform for community engagement and development. We selected Camp Hill Borough, PA, as a case study to analyze building-specific energy performance and evaluate the electrification potential of each building by switching to different Heating, Ventilation, and Air Conditioning (HVAC) systems and measurement components. The simulation results generated by the workflow provide retrofitting suggestions to help mitigate the carbon footprint as well as energy saving statistics of buildings. Additionally, the developed web-based interface serves as a community engagement platform, allowing residents to provide feedback and further develop interactive communication protocols. The outcomes of this project offer a baseline for community electrification planning and contribute to the design of low-carbon communities.

Chowdhury, Shovan [ORNL]↗

DOE OSTI2026

Structure-function analysis of the FCRL5–IgG1 Fc complex reveals an unappreciated pathway for B cell modulation by Fc-attenuated IgG

The Fc region of therapeutic IgG antibodies is often engineered to remove or “silence” Fc effector functions, but it remains unclear whether these mutations eliminate all Fc-mediated effector activity. Human Fc receptor-like 5 (FCRL5/FcRH5) is a low-affinity IgG Fc receptor expressed on B cells and is an actively pursued antibody target in multiple myeloma. Here, we show that common Fc function-silencing mutations do not impair FCRL5-mediated activity and therefore attenuate, rather than eliminate, Fc effector function. The crystal structure of the FCRL5-IgG1 Fc complex, solved at 3.4 Å resolution, revealed that FCRL5 binds IgG1 Fc in a 1:1 complex through a binding mode distinct from that of classical Fcγ receptors, explaining why mutations that attenuate Fc effector function spare FCRL5 binding. Fc-engineered antibodies that selectively engage FCRL5 inhibited B cell receptor-induced Ca 2+ flux in FCRL5-expressing B cells. These findings demonstrate that Fc-attenuated therapeutic IgG retains the ability to engage FCRL5, identifying an unappreciated pathway for B cell modulation.

Herpers, Bart M. [Department of Biomedical Enginee↗

DOE OSTI2025

CpoS-Inc interactions facilitate host cell modulation during Chlamydia trachomatis infection

ABSTRACT Chlamydia trachomatis ( C.t .), the leading bacterial cause of sexually transmitted infections, replicates within a unique intracellular compartment called the inclusion, which is modified by secreted proteins known as inclusion membrane (Inc) proteins. Here, we further characterize CpoS, an Inc protein previously shown to be critical for bacterial replication and inclusion development. We demonstrate that CpoS directly binds multiple coiled-coil region-containing Incs and engages Rab GTPases at a separate site. Notably, CpoS-InaC interactions facilitate the recruitment of select Arf GTPases to the inclusion membrane, while Rab recruitment occurs independently of these interactions. Biochemical and biophysical analyses revealed that Incs self-oligomerize to form higher-ordered structures, with CpoS adopting a tetrameric conformation resembling that of eukaryotic SNARE proteins. We propose that these assemblies serve as scaffolds to orchestrate vesicle docking, tethering, and fusion. Our findings highlight the intricate interplay between bacterial and host factors, revealing how C.t . leverages both Inc-Inc interactions and host protein engagement to manipulate vesicular trafficking and sustain infection.

Tijerina, Xavier [Department of Microbiology and I↗

DOE OSTI2020

Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism

Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Bridging the Gap between Analytical and Microbial Sciences in Microbiome Research

Metabolites from the microbiome influence human, animal, and environmental health, but the diversity and functional roles of these compounds have only begun to be elucidated. Comprehensively characterizing these molecules are significant challenges, as it requires expertise in analytical methods, such as mass spectrometry and nuclear magnetic resonance spectroscopy, skills that not many traditional microbiologists or microbial ecologists possess. This creates a gap between microbiome scientists that want to understand the role of microbial metabolites in microbiome systems and the skills required to generate and interpret complex metabolomics data sets. To bridge this gap, microbiome scientists should engage analytical chemists to best understand the underlying chemical principles of the data. Conversely, analytical scientists are encouraged to engage with microbiome scientists to better understand the biological questions being asked with metabolomics and to best communicate its intricacies. Better communication across the chemistry/biology disciplines will further reveal the “dark matter” within microbiomes that maintain healthy humans and environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Repometer v.1.0

SAND2022-4256 O Online version control platforms offer insight into traffic and engagement with source code repositories, but only in limited ways and over short windows of time. Scientific software teams at Sandia National Laboratories and elsewhere want to collect and store engagement data to help tell their story and the impact their work has on the community. Repometer aims to supplement existing capabilities by collecting timely and insightful data from GitHub and GitLab repositories and passing it to a database for longer-term storage. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Mundt, Miranda↗

DOE OSTI2023

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗

DOE OSTI2024

Discovery of BBO-8520, a First-In-Class Direct and Covalent Dual Inhibitor of GTP-Bound (ON) and GDP-Bound (OFF) KRASG12C

Abstract Approved inhibitors of KRASG12C prevent oncogenic activation by sequestering the inactive, GDP-bound (OFF) form rather than directly binding and inhibiting the active, GTP-bound (ON) form. This approach provides no direct target coverage of the active protein. Expectedly, adaptive resistance to KRASG12C (OFF)-only inhibitors is observed in association with increased expression and activity of KRASG12C(ON). To provide optimal KRASG12C target coverage, we have developed BBO-8520, a first-in-class, direct dual inhibitor of KRASG12C(ON) and (OFF) forms. BBO-8520 binds in the Switch-II/Helix3 pocket, covalently modifies the target cysteine, and disables effector binding to KRASG12C(ON). BBO-8520 exhibits potent signaling inhibition in growth factor–activated states, in which current (OFF)-only inhibitors demonstrate little measurable activity. In vivo, BBO-8520 demonstrates rapid target engagement and inhibition of signaling, resulting in durable tumor regression in multiple models, including those resistant to KRASG12C(OFF)-only inhibitors. BBO-8520 is in phase 1 clinical trials in patients with KRASG12C non–small cell lung cancer. Significance: BBO-8520 is a first-in-class direct, small molecule covalent dual inhibitor that engages KRASG12C in the active (ON) and inactive (OFF) conformations. BBO-8520 represents a novel mechanism of action that allows for optimal target coverage and delays the emergence of adaptive resistance seen with (OFF)-only inhibitors in the clinic. See related commentary by Zhou and Westover, p. 455

Oncology↗

DOE OSTI2021

The Making of a Metric: Co-Producing Decision-Relevant Climate Science

Developing decision-relevant science for adaptation requires the identification of climatic parameters that are both actionable for practitioners as well as tractable for modelers. In many sectors, these decision-relevant climatic metrics and the approaches that enable their identification remain largely unknown. “Co-production” of science with scientists and decision-makers is one potential way to identify these metrics, but there is little research describing specific and successful co-production approaches. This paper examines the negotiations and outcomes from Project Hyperion, wherein scientists and water managers jointly developed decision-relevant climatic metrics for adaptive water management. We identify successful co-production strategies by analyzing the project’s numerous back-and-forth engagements and tracing the evolution of the science during these engagements. We found that effective mediation between scientists and managers needed dedicated “boundary spanners” with significant modeling expertise. Translating practitioners’ information needs into tractable climatic metrics required direct and indirect methods of eliciting knowledge. We identified four indirect methods that were particularly salient for extracting tacitly held knowledge and enabling shared learning: developing a hierarchical framework linking management issues with metrics, starting discussions from the planning challenges, collaboratively exploring the planning relevance of new scientific capabilities, and using analogies of other “good” metrics. The decision-relevant metrics we developed provide insights into advancing adaptation-relevant climate science in the water sector. The co-production strategies we identified can be used to design and implement productive scientist–decision-maker interactions. Overall, the approaches and metrics we developed can help climate science to expand in new and more use-inspired directions.

Planning↗

DOE OSTI2025

Advancing Urban Water Resilience: Coproducing Knowledge through Civic–Academic Global Partnerships on Water and Climate

As extreme weather events become more pronounced, the vulnerabilities associated with the urban water supply and wastewater systems in megacities are intensified in multiple interconnected dimensions. These multifaceted water challenges can benefit from enhanced cross-sectoral collaboration and sharing of critical knowledge, which are essential for sustainable and adaptive water governance frameworks. In this context, the Megacity Alliance for Water and Climate (MAWAC)–Europe and North America Region (ENAR) Working Group convened a workshop in March 2023, followed by a subsequent workshop in London, United Kingdom, from 11 to 13 September 2024. These workshops aimed to investigate and devise solutions for the cascading hazards with water systems. The solutions examined various aspects focused on climate adaptation and mitigation, stormwater management, and the governance of water and wastewater systems. Additionally, discussions highlighted the importance of community engagement, economic considerations, equity, and effective communication in addressing these pressing challenges. Over the course of 3 days, experts from academia, government agencies, and industry engaged in meaningful discussions on digital modeling for integrated water management, climate-informed urban planning, and public–private–academic partnerships (Fig. 1). Case studies from cities such as New York, Los Angeles, London, Paris, and Chicago highlighted innovative governance strategies for managing water and wastewater systems, promoting water reuse, planning infrastructure, and fostering stakeholder-driven and stakeholder-informed adaptation. The workshop participants emphasized the need for data-driven decision-making, scalable governance models, and knowledge-sharing networks to enhance urban water governance for sustainability and resilience. This workshop report presents the key takeaways from the 3-day convening, providing a roadmap for integrating scientific research, policy frameworks, and emerging technologies to address water challenges faced by megacities.

Hydrologic models↗

DOE OSTI2024

Development and Outcomes of Returning Polycyclic Aromatic Hydrocarbon Exposure Results in the Washington Heights, NYC Community

Report-back of research results (RBRR) is becoming standard practice for environmental health research studies. RBRR is thought to increase environmental health literacy (EHL), although standardized measurements are limited. For this study, we developed a report back document on exposure to air pollutants, Polycyclic Aromatic Hydrocarbons, during pregnancy through community engaged research and evaluated whether the report increased EHL. We used focus groups and surveys to gather feedback on the report document from an initial group of study participants (Group 1, n = 22) and then sent the revised report to a larger number of participants (Group 2, n = 168). We conducted focus groups among participants in Group 1 and discussed their suggested changes to the report and how those changes could be implemented. Participants in focus groups demonstrated multiple levels of EHL. While participant engagement critically informed report development, a survey comparing feedback from Group 1 (initial report) and Group 2 (revised report) did not show a significant difference in the ease of reading the report or knowledge gained about air pollutants. We acknowledge that our approach was limited by a lack of EHL tools that assess knowledge and behavior change, and a reliance on quantitative methodologies. Future approaches that merge qualitative and quantitative methodologies to evaluate RBRR and methodologies for assessing RBRR materials and subsequent changes in knowledge, attitudes, and behavior, may be necessary.

Children’s Environmental Health↗