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Chapter 5: Major Biological Innovations in the History of Life on Earth

All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA—the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. Here this chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell—the eukaryotic cell—which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scaling Decarbonization Development Innovation with Emerging Community-Based Developers: Preprint

The building real estate development industry is being asked to lead in delivering building decarbonization solutions across the United States. However, creating decarbonized best practices and development innovation while increasing developer diversity and community ownership is often not a primary focus of this sector. To address these issues, we have created an incubator and support ecosystem specifically for the innovation scaling we have found in a leading group of emerging, small-scale developers. These leaders are not just working at the forefront of decarbonized development but addressing diversity and bolstering community generational wealth. We have found that small development firms are the ones who often take risks to innovate and demonstrate despite lacking a specific set of resources or support ecosystems focused on emerging decarbonization developers. Those with the fewest resources are being asked to lead our decarbonization innovation efforts. This paper documents the necessity of a cohort and incubator program to provide a decarbonization-specific ecosystem to support small developers and scale innovation. The incubator creates connections, fosters innovative strategies to access incentives and alternative funding, and assembles resources for small and emerging minority developers with the goal of sustainability and affordability. For instance, collaborative efforts with leading developers and utilities can enable the seamless integration of distributed energy resources through optimal metering and interconnection and significantly reduce the utility cost of electrification, benefiting the utility, the developer, and the tenant economically. The process described in this paper will result in case studies and how-to resources to provide tangible examples of innovation within the emerging development field.

carbon↗

Enhancing Radionuclide Production Capabilities at the Duke University Medical Center Cyclotron with a Focus on Astatine-211

Radionuclides play an important role in a diverse array of fields including physics, chemistry, agriculture, materials science, national security, medical research and patient care. Establishing a reliable domestic supply of key radionuclides is critical to our national competitiveness in these areas. Regarding medical applications, targeted alpha-particle therapy (TAT) has become of great interest to basic researchers and clinicians alike and is emerging as a valuable and cost-effective approach for cancer treatment. Unfortunately, progress in TAT, particularly with regard to its clinical translation, has been severely hampered by the limited availability of the most promising radionuclides at a reasonable cost, and with appropriate chemical and radiochemical purity. In this project, we have attempted to address this problem by focusing on production of the 7.2-h half-life α-particle emitter, 211 At, which has long been considered to be one of the most promising radionuclides for TAT. We note that he critical importance of improving the supply of 211 At in the United States was noted in the Funding Opportunity Announcement related to this project. At Duke University, we have a CS-30 cyclotron that is one of the few accelerators in the United States that has an alpha-particle beam that has enough energy to make useful quantities of 211 At. With this cyclotron, we have been able to produce more 211 At than anywhere else in the world because of our unique internal cyclotron target system. However, the CS-30 cyclotron is nearly 40 years old and was no longer reliable. In addition, its operation required considerable skill, largely because it had analog control systems, and vital parts including old-fashioned power supplies, were becoming unavailable. For these reasons, the current project was undertaken to evaluate all the subsystems of the CS-30 cyclotron and replace, repair, and update them. With help from our consultant, Ionetix, this has now been accomplished. We believe that because of this work, the CS-30 can reliably supply 211 At for basic research and clinical trials both at Duke and beyond.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Habitat severity characteristics structure soil communities at regional and local spatial scales along the Antarctica Peninsula

Antarctic soils provide an excellent setting to test biogeographical patterns across spatial and environmental scales given their relatively simple communities and the dominance of physical factors that create strong environmental gradients. Additional urgency is given by the fact that their unique terrestrial communities are the subject of conservation efforts in a rapidly changing environment. We investigated relationships of soil community assembly and alpha and beta diversity with climatic and environmental parameters across regional and local scales in Maritime Antarctica. We sampled from a regional gradient of sites that differ in habitat severity, ranging from relatively favourable to harsher physicochemical conditions. At the regional scale, bacterial community characteristics and microarthropod abundance varied along this severity gradient, but most measures of fungal communities did not. Microarthropod and microbial communities differed in which soil and climate parameters were most influential, and the specific parameters that influenced each taxon differed across broad and fine spatial scales. This suggests that conservation efforts will need to focus on a large variety of habitat characteristics to successfully encompass diversity across taxa. Because beta diversity was the result of species turnover, conservation efforts also cannot focus on only the most biodiverse sites to effectively preserve all aspects of biodiversity.

54 ENVIRONMENTAL SCIENCES↗

Genomic insights into local adaptation and migration success in reintroduced Coho Salmon of the Wenatchee River basin

ABSTRACT Objective Reintroduction of salmonids into regions where they have been extirpated is a common conservation strategy that is often implemented through natural recolonization, translocation of natural populations, or hatchery-based programs. Locally adapting to specific environmental conditions is critical for long-term population viability, particularly for species like Coho Salmon Oncorhynchus kisutch, which face diverse selective pressures during their migration. This study focused on the mid-Columbia River Coho Salmon reintroduction program managed by Yakama Nation Fisheries, which has successfully reintroduced Coho Salmon into the Wenatchee and Methow River basins, Washington. Notably, these populations have adapted to the longer migration route than those in the founding stock, with selection favoring individuals with an earlier arrival time and that can navigate a 15-km, high-gradient canyon to reach optimal spawning grounds. The objectives of this study were to investigate whether specific genomic regions are under selection for traits associated with return location and timing in Coho Salmon. Methods Low-coverage whole-genome resequencing data were used to screen for genomic regions associated with the phenotypes of interest. Results A weak polygenic signal in female Coho Salmon was found to be associated with return group, with a subset of candidate adaptive regions occurring across eight chromosomes. Conclusions These findings provide insights into the genomic mechanisms underlying local adaptation in reintroduced salmon populations and inform broodstock selection strategies aimed at promoting natural production and long-term population sustainability.

Horn, Rebekah L.↗

Impact of Inverter-Based Resources on Grid Protection: A Review of Negative-Sequence Current Generation

The increasing integration of inverter-based resources (IBRs) in power grids poses challenges to traditional protection systems, primarily due to their different fault current signatures compared to conventional synchronous generators. Unlike synchronous generators whose fault response is dictated by their physical design, IBRs exhibit a wide range of fault characteristics due to manufacturer-specific control algorithms and settings. This dependence on proprietary control schemes makes modeling IBR behavior during faults significantly more complex, especially considering the rapid evolution of inverter technology and the diverse control strategies employed. While much research has focused on the positive-sequence current injections of IBRs during symmetrical faults, the understanding of negative-sequence current generation during non-symmetrical faults remains limited. This report provides an overview of current research on IBRs' negative-sequence current generation during unbalanced faults and its impact on protection schemes based on negative-sequence components. It covers both type III wind turbines and full-size converter-based IBRs. Additionally, this report reviews strategies for grid-forming controlled inverters to generate negative-sequence current during unbalanced faults, in addition to grid-following controlled ones.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Chemical Characterization and Antimicrobial Activity of Green Propolis from the Brazilian Caatinga Biome

Green propolis, particularly from the unique flora of the Brazilian Caatinga biome, has gained significant interest due to its diverse chemical composition and biological activities. This study focuses on the chemical characterization and antimicrobial evaluation of Caatinga green propolis. Twelve compounds were isolated through different chromatographic techniques, including flavanones (naringenin, 7-O-methyleriodictyol, sakuranetin), flavones (hispidulin, cirsimaritin), flavonols (quercetin, quercetin-3-methyl ether, kaempferol, 6-methoxykaempferol, viscosine, penduletin), and one chalcone (kukulkanin B). Using liquid chromatography–quadrupole time-of-flight tandem mass spectrometry (LC-QToF-MS), a total of 55 compounds excluding reference standards were tentatively identified, which include flavonoids, phenolic acids derivatives, and alkaloids, with flavonols, flavanones, and flavones being predominant. Antimicrobial testing against pathogens revealed that the crude extract exhibited low inhibitory activity, against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE) (IC50: 148.4 and 120.98 µg/mL, respectively). Although the isolated compounds showed limited individual activity, a fraction containing sakuranetin and penduletin (Fraction 8) exhibited moderated activity against Cryptococcus neoformans (IC50: 47.86 µg/mL), while a fraction containing quercetin and hispidulin showed moderated activity against VRE (IC50: 16.99 µg/mL). These findings highlight the potential application of Caatinga green propolis as an antimicrobial agent, particularly against resistant bacterial strains, and underscore the importance of synergistic interactions between compounds in enhancing biological effects.

Aldana-Mejía, Jennyfer A. (ORCID:0000000307361899)↗

Application of the FaMUS Methodology to the NSUF Research Outputs Through End of 2019

The Nuclear Science User Facilities (NSUF) is one of a diverse group of DOE user facilities. It is focused on advancing the understanding of radiation effects in nuclear fuels and materials in support of nuclear energy applications. The NSUF has been operating since 2007 and has developed a significant portfolio of supported research. Therefore, it is appropriate to consider its achievements and to determine its successes and shortfalls. As part of this analysis of the NSUF research program, the NSUF has developed a novel and elegant formalism for assessing the current level of understanding of nuclear fuels and materials for use in nuclear environments: the NSUF Fuels and Materials Understanding Scale (FaMUS). The FaMUS methodology is being applied to the NSUF portfolio on an ongoing basis to quantify the progress made. This report summarizes the status of the assessment exercise and highlights general lessons learned. This examination will facilitate capability balancing of future research by identifying gaps in knowledge, understanding, testing, and demonstration allowing the NSUF program office in conjunction with DOE-NE to direct resources to important aspects of the DOE-NE mission using “emphasize & enhance”, “maintain”, and “encourage excellence” classifications as well as providing increased transparency to researchers.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Advanced Fuels Campaign Execution Plan

The Advanced Fuels Campaign (AFC) Execution Plan details the strategy, mission, scope, and goals—both near-term and long-term—along with the structure and organization of nuclear fuels and materials research, development, and demonstration (RD&D) activities within the Fuel Cycle Technologies (FCT) program. The FCT program, tasked by the U.S. Department of Energy (DOE), employs a science-based approach to advance fuel technologies. This approach integrates theory, experiments, and multi-scale modeling and simulation (M&S) to develop a predictive understanding of fuel fabrication processes and fuel/cladding performance under irradiation, moving beyond traditional empirical methods. The long-term goals of the AFC are guided by the AFC Strategic Plan and align with the DOE Office of Nuclear Energy (NE) Roadmap [1], which outlines a multi-decade vision for demonstrating and qualifying advanced fuel forms to support diverse fuel cycle options. Near-term goals focus on enhancing accident tolerant fuels (ATF) for Light Water Reactors (LWR), a significant challenge that demands balancing immediate objectives with ongoing progress toward advanced reactor missions. Accelerating the traditional fuel qualification process to meet ATF objectives is another critical challenge. A detailed set of 5-year goals, summarized below, has been developed in line with the overarching science-based fuel development approach: • Advanced LWR Fuel Technologies: By 2027, support the development of advanced LWR fuel technologies with improved performance and enhanced accident tolerance. This includes high burnup (HBu), low enriched uranium (LEU)+, coated cladding, and doped fuel, aimed at complementing industry-led significant LWR uprates and plant refurbishments. • Tristructural Isotropic (TRISO) Fuel: Achieve qualification by 2028 and develop improved designs for emerging markets. • Metal Fuel: Achieve qualification by 2028 and develop improved designs for emerging markets. • Molten Salt Fuel: By 2027, deploy a robust program that enables fuel salt qualification technologies needed to support fuel salt research and development (R&D), focusing on emergent needs to derisk fuel salt production and utilization in advanced reactors. • Long-Term ATF: Develop fuel technologies that enable significant power uprates (~50%) in refurbished or new LWRs while optimizing fissile material utilization and waste disposal. The 5-year milestones in the AFC Execution Plan are contingent on an assumed budget. This Execution Plan will be updated annually to reflect actual funding profiles as budget guidance becomes available, ensuring milestones are adjusted accordingly. In summary, the AFC Execution Plan presents a comprehensive strategy to advance nuclear fuel technologies through a science-based approach, addressing both near-term and long-term goals while adapting to funding realities.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

Editorial: Microbial C1 Metabolism and Biotechnology

Archaea and bacteria with the capacity to utilize one-carbon (C1) molecules as carbon and energy sources are widespread across the planet and are important players in many biogeochemical processes. As such, they occupy an array of diverse anaerobic and aerobic niches and perform unique metabolisms that enable the utilization of carbon dioxide (CO 2 ), carbon monoxide (CO), formate (HCOOH), methanol (CH 3 OH), and methane (CH 4 ) for growth. Several industrial processes have been developed that leverage these microbes for the targeted conversion of anthropogenic waste gases that contain C1 molecules, including natural gas (CH 4 ), anaerobic digestion-derived biogas (CH 4 and CO 2 ), industrial flue gas (CO 2 and CO), and syngas (CO 2 , CO, and H 2 ) (Figure 1). Further, there is increasing interest in electrochemical reduction of CO 2 to CO, CH 4 , and intermediates with increased solubility compared to gaseous C1 molecules (formate and methanol) using electrons derived from renewable sources like wind, solar, or hydrothermal systems to mitigate atmospheric greenhouse gas. Thus, C1-utilizing microbes will likely play an integral role in biotechnologies that are part of a sustainable, circular bioeconomy. However, fundamental knowledge gaps into the metabolism and physiology of these microbes exist that limit their utility as biocatalysts for carbon-efficient biomanufacturing. This special topic presents studies focused on the fundamental aspects of C1 metabolism in diverse microbial systems with the ability to convert anthropogenic greenhouse gases into valuable products.

59 BASIC BIOLOGICAL SCIENCES↗

Scenario Storyline Discovery for Planning in Multi‐Actor Human‐Natural Systems Confronting Change

Scenarios have emerged as valuable tools in managing complex human-natural systems, but the traditional approach of limiting focus on a small number of predetermined scenarios can inadvertently miss consequential dynamics, extremes, and diverse stakeholder impacts. Exploratory modeling approaches have been developed to address these issues by exploring a wide range of possible futures and identifying those that yield consequential vulnerabilities. However, vulnerabilities are typically identified based on aggregate robustness measures that do not take full advantage of the richness of the underlying dynamics in the large ensembles of model simulations and can make it hard to identify key dynamics and/or storylines that can guide planning or further analyses. This study introduces the FRamework for Narrative Storylines and Impact Classification (FRNSIC; pronounced “forensic”): a scenario discovery framework that addresses these challenges by organizing and investigating consequential scenarios using hierarchical classification of diverse outcomes across actors, sectors, and scales, while also aiding in the selection of scenario storylines, based on system dynamics that drive consequential outcomes. We present an application of this framework to the Upper Colorado River Basin, focusing on decadal droughts and their water scarcity implications for the basin's diverse users and its obligations to downstream states through Lake Powell. We show how FRNSIC can explore alternative sets of impact metrics and drought dynamics and use them to identify drought scenario storylines, that can be used to inform future adaptation planning.

54 ENVIRONMENTAL SCIENCES↗

Cellulose-MOFs hybrid materials: Chemistry and mechanism of applications in biomedical - A review

Rising costs and performance limits of modern biomedical materials motivate the search for advanced, biocompatible alternatives. Cellulose-based metal-organic frameworks (cellulose-MOFs) emerge as distinctive hybrids combining renewable polymer chemistry with tunable porous architectures, enabling uncommon structure–function relationships. Their large surface area, controllable pore size, adaptable functional groups, and efficient host–guest interactions underpin diverse biomedical functions. Till now, no comprehensive, application-focused review has systematically summarized cellulose-MOFs synthesis for biomedical applications. This review critically analyzes cellulose-MOFs, emphasizing mechanistic links between chemistry, synthesis routes, interfacial interactions, and biomedical performance, rather than cataloging applications alone. Antibacterial action, targeted drug delivery, and sensing/biosensing are discussed through comparative insights. The article identifies unresolved challenges and proposes future research pathways to rationally design next-generation cellulose-MOFs systems, guiding researchers and clinicians alike.

Biomedical↗

Environmental design of low-head run-of-river hydropower in the United States: A review of facility design models

We state that the goal of run-of-river hydropower is to produce cost-competitive renewable electricity with minimal disruption of the natural riverine ecosystem. Modeling and feasibility analysis of alternative design options are crucial for developing new run-of-river hydropower projects. Our review shows that existing run-of-river hydropower design models focus on maximizing economic potential at high-head diversion schemes with limited consideration of environmental outcomes. Since nearly three-quarters of new hydropower potential in the United States is found at low-head sites and environmental performance standards are imperative to project success, new models are needed to address the multi-dimensional design challenges at these sites. To aid in formulating holistic models, we synthesize the performance objectives and design variables related to early-stage run-of-river facility design. The objectives span six potential impact areas, including hydrologic alteration, sediment continuity, water quality, aquatic species passage, social, and economic. Based on these reviews, we identify three key areas to enhance the capabilities of run-of-river hydropower design models. These are 1) expanded model formulations, 2) assessment of barrier effects, and 3) explicit environmental objectives. The resulting modeling improvements would accelerate the identification of run-of-river hydropower designs that minimize environmental impacts, promote economic competitiveness, and incorporate the value of non-power benefits.

13 HYDRO ENERGY↗

Elemental zoning enhances mass transport in zeolite catalysts for methanol to hydrocarbons

Mass transport limitations in zeolite catalysts pose major hurdles for their optimal performance in diverse chemical reactions. Most approaches to reduce these restrictions focus on the synthesis of either hierarchical or nanosized zeolites. Here we demonstrate that the existence of a siliceous, catalytically inactive exterior rim on ZSM-5 particles dramatically reduces the diffusion limitations, which leads to an enhanced catalyst lifetime for the methanol-to-hydrocarbon reaction. In this study, our findings reveal that binary inorganic and organic structure-directing agents enable a one-pot synthesis of Si-zoned ZSM-5 catalysts with diffusion properties that are characteristic of particles with a much smaller size. Operando ultraviolet–visible light diffuse reflectance spectroscopy reveals a marked reduction in external coking among Si-zoned samples. Molecular dynamics simulations to assess the diffusion of methanol and benzene in siliceous pores and in those with Brønsted acids reveal substantially reduced transport limitations in zoned regions, consistent with the improved catalyst activity of Si-zoned zeolites relative to that of ZSM-5 with a homogeneous acid-site distribution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

metagRoot: a comprehensive database of protein families associated with plant root microbiomes

The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.

Chasapi, Maria N↗

Discovering Innovations in Stress Tolerance through Comparative Gene Regulatory Network Analysis and Cell-Type Specific Expression Maps (Final Technical Report with Cover Page)

Through this grant, we developed a comparative framework to elucidate the mechanisms behind variations in environmental stress responses among a diverse group of species within the Brassicaceae family. Our focus was on the differences in physiological and transcriptomic responses to abscisic acid (ABA), a hormone associated with water stress. We examined the differential growth responses of four Brassicaceae species, finding that most exhibited reduced root growth correlated with smaller meristem size. In contrast, Schrenkiella parvula showed accelerated growth due to increased root cell elongation. We employed RNA sequencing to analyze the transcriptional responses to ABA across these species, and innovative bioinformatics techniques were used to pinpoint biological pathways with significant divergence. Additionally, we utilized DAP-seq to map the gene regulatory networks associated with ABAresponsive transcription factors, revealing that variations in the regulation of growth hormone biosynthesis play a critical role in the distinct ABA effects on root growth among the species. This research sets a new standard for comparative physiology by integrating comparative genomics and transcriptomics to uncover pathway divergences.

59 BASIC BIOLOGICAL SCIENCES↗