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DOE OSTI2022

The Structure and Immune Regulatory Implications of the Ubiquitin-Like Tandem Domain Within an Avian 2’-5’ Oligoadenylate Synthetase-Like Protein

Post-translational modification of host and viral proteins by ubiquitin and ubiquitin-like proteins plays a key role in a host’s ability to mount an effective immune response. Avian species lack a ubiquitin-like protein found in mammals and other non-avian reptiles; interferon stimulated gene product 15 (ISG15). ISG15 serves as a messenger molecule and can be conjugated to both host and viral proteins leading them to be stabilized, degraded, or sequestered. Structurally, ISG15 is comprised of a tandem ubiquitin-like domain (Ubl), which serves as the motif for post-translational modification. The 2’-5’ oligoadenylate synthetase-like proteins (OASL) also encode two Ubl domains in series near its C-terminus which binds OASL to retinoic acid inducible gene-I (RIG-I). This protein-protein interaction increases the sensitivity of RIG-I and results in an enhanced production of type 1 interferons and a robust immune response. Unlike human and other mammalian OASL homologues, avian OASLs terminate their tandem Ubl domains with the same LRLRGG motif found in ubiquitin and ISG15, a motif required for their conjugation to proteins. Chickens, however, lack RIG-I, raising the question of structural and functional characteristics of chicken OASL (chOASL). By investigating chOASL, the evolutionary history of viruses with deubiquitinases can be explored and drivers of species specificity for these viruses may be uncovered. Here we show that the chOASL tandem Ubl domains shares structural characteristics with mammalian ISG15, and that chOASL can oligomerize and conjugate to itself. In addition, the ISG15-like features of avian OASLs and how they impact interactions with viral deubiquitinases and deISGylases are explored.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Nanostructures for Electrical Energy Storage (NEES) (2020 Final Technical Report)

Nanostructures for Electrical Energy Storage (NEES, www.efrc.umd.edu) was an Energy Frontier Research Center supported by the DOE Office of Science, Basic Energy Sciences, from 8/1/2009 to 7/31/2020. Led by the University of Maryland, NEES enjoyed extensive collaborations with its funded partners, including two DOE Laboratories and six universities. The NEES vision has been to reveal a set of scientific insights and design principles that can underpin a next-generation electrical energy storage approach, building on advances in nanoscale science and technology to achieve simultaneous high power and high energy over extended charge/discharge cycling. The vision is motivated by the recognition that scaling into the nano regime opens the door to new physical phenomena and that the tools enlisted in nanoscale research provide major new opportunities for the synthesis not only of materials at molecular scale but for structures at nano scale and above. NEES has translated this vision into its research program based on two observations. First, while the behavior of ions and electrons in electrolytes and in electrode materials is crucial to electrical energy storage (or more appropriately electrochemical energy storage), it is the transport of ion and electron charge between different structural components of a storage device that ultimately determine its performance. With it well recognized that the choice of electrode materials typically constrain ion transport kinetics as well as maximum ion concentration, the search for better electrode materials has been a primary driver of battery research. At the same time the synthesis of electrodes is typically based on aggregation of particles with varying size, shape, and orientation in the electrode. Together with the presence of additional materials to impart electrical conductivity and cohesion to the composite electrode, change in electrode materials is necessarily accompanied by structural changes at the nano/micro scale that are difficult to categorize and manage. From the beginning, NEES’ vision has been to create and study simpler, highly controlled spatial arrangements of known materials as battery components (electrodes, current collectors, and electrolyte) and to understand how design and structure above the molecular scale determines the energy storage performance available from known materials. Second, advances in nanoscience dramatically expanded the portfolio of synthesis methods, structural motifs, and new phenomena available for research. Some of these gave rapid access to new building blocks at the deep nanoscale (e.g., carbon nanotubes grown by self-assembly, nanoscale arrays formed by electrochemical self-alignment, monolayer films controlled by self-limiting reaction). Such advances served as the enabler for the NEES vision to be pursued experimentally through study of 3D structures created and controlled at the nano, micro, and meso scales. Here, we use meso as in the BES MESO Report, implying not only intermediate or varying length scales, but very much the way behavior is influenced by other factors including aggregation of nanocomponents at different densities and spatial configurations, statistical variations in the aggregates, hierarchical architectures in which they can be assembled, or local 3D configurations that result from the architectures. Over its life cycle, NEES has pursued two overarching goals: (1) to understand the scientific fundamentals of electrochemical storage from the nanoscale to the mesoscale; and (2) to create and learn from innovative, controlled, heterogeneous nanostructures, where such nanostructures can enable the first goal and serve as models for future paradigms in energy storage. Specific goals have included: Synthesize heterogeneous nanostructures comprised of multiple materials arranged in controlled fashion and characterize their behavior; Demonstrate and elucidate design principles for achieving simultaneous high power and high energy; Develop materials processes which enable precision control of thin layers and 3D structures; Investigate the impact of artificial interphases on electrode stability during ion insertion/deinsertion; Create dense arrays of nanostructures to understand how the architecture of these assemblies, along with nanostructure design, influences energy storage behavior at the mesoscale; Identify and understand the consequences of nanoconfinement and local inhomogeneities in 3D mesoscale arrays; Develop and apply computational models to stimulate, guide and interpret experiments.

25 ENERGY STORAGE↗

NASA NTRS1998

Visually induced adaptation in three-dimensional organization of primate vestibuloocular reflex

The adaptive plasticity of the spatial organization of the vestibuloocular reflex (VOR) has been investigated in intact and canal-plugged primates using 2-h exposure to conflicting visual (optokinetic, OKN) and vestibular rotational stimuli about mutually orthogonal axes (generating torsional VOR + vertical OKN, torsional VOR + horizontal OKN, vertical VOR + horizontal OKN, and horizontal VOR + vertical OKN). Adaptation protocols with 0.5-Hz (+/-18 degrees ) head movements about either an earth-vertical or an earth-horizontal axis induced orthogonal response components as high as 40-70% of those required for ideal adaptation. Orthogonal response gains were highest at the adapting frequency with phase leads present at lower and phase lags present at higher frequencies. Furthermore, the time course of adaptation, as well as orthogonal response dynamics were similar and relatively independent of the particular visual/vestibular stimulus combination. Low-frequency (0. 05 Hz, vestibular stimulus: +/-60 degrees ; optokinetic stimulus: +/-180 degrees ) adaptation protocols with head movements about an earth-vertical axis induced smaller orthogonal response components that did not exceed 20-40% of the head velocity stimulus (i.e., approximately 10% of that required for ideal adaptation). At the same frequency, adaptation with head movements about an earth-horizontal axis generated large orthogonal responses that reached values as high as 100-120% of head velocity after 2 h of adaptation (i.e., approximately 40% of ideal adaptation gains). The particular spatial and temporal response characteristics after low-frequency, earth-horizontal axis adaptation in both intact and canal-plugged animals strongly suggests that the orienting (and perhaps translational) but not inertial (velocity storage) components of the primate otolith-ocular system exhibit spatial adaptability. Due to the particular nested arrangement of the visual and vestibular stimuli, the optic flow pattern exhibited a significant component about the third spatial axis (i.e., orthogonal to the axes of rotation of the head and visual surround) at twice the oscillation frequency. Accordingly, the adapted VOR was characterized consistently by a third response component (orthogonal to both the axes of head and optokinetic drum rotation) at twice the oscillation frequency after earth-horizontal but not after earth-vertical axis 0.05-Hz adaptation. This suggests that the otolith-ocular (but not the semicircular canal-ocular) system can adaptively change its spatial organization at frequencies different from those of the head movement.

Non-NASA Center↗

DOE OSTI2022

Crystal Ball: A Naturalist Perspective of Microbiology: Examples from Methanogenic Archaea

Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Naturalists are scientists that tell stories of organisms and their natural environment within a historical context and from an interdisciplinary perspective. Such stories interweave observations of biological subjects from disparate disciplines into a cohesive story. To this end, the success of naturalists in recounting compelling natural history stories is enhanced when they allow themselves to become vulnerable by knowingly entering a literature base full of unfamiliar ways of observing and describing such subjects. When successful, this approach can broaden the scope of the story, making it of interest to a larger audience and attracting further recounting of that story (e.g., citations). To this end, when we look into our crystal ball, we see a need to tell more holistic stories of microorganisms and their functions from an interdisciplinary, naturalist perspective that combines what is known of their contemporary ecology, physiology, and biochemistry with their evolutionary history thereby placing them within a historical Earth context. With this conviction in mind, we take the opportunity to look back on the natural history of methanogens to identify some of their most profound biochemical innovations and their impact on the trajectory of life and the planet. Our approach was to integrate knowledge from the fields of biochemistry, physiology, ecology, evolution, geochemistry, and atmospheric sciences. We start with the origin of the first autotrophic cells and how this set Earth on a path towards biomass expansion and functional diversification. Next, we discuss the importance of iron and sulfur in methanogen metabolism, and how their innovative ways of accessing these elements allowed for expanded use of iron-sulfur clusters ([Fe-S]) as nanoscale catalysts that power(ed) Earth’s biochemical cycles. We next discuss the origin and evolution of [NiFe]-hydrogenase and how this versatile enzyme chassis was co-opted by a variety of anaerobes and aerobes as the foundation for respiratory complexes capable of sustaining higher forms of life, including humans. Lastly, we discuss the evolution of the enzyme molybdenum nitrogenase, and how this allowed the biosphere to overcome fixed nitrogen limitation by tapping the seemingly endless reserve of atmospheric dinitrogen (N 2 ). In telling these stories, we aimed to generate template(s) to motivate future interdisciplinary natural history studies focused on other organisms and processes. Further, we hope to stimulate scientific discourse and provide impetus to become vulnerable and peruse literature of relevance to understanding the causes and consequences of the evolution of your favorite microorganism or biochemical process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Global Methane Budget 2000–2020

Abstract. Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. CH4 is the second most important human-influenced greenhouse gas in terms of climate forcing after carbon dioxide (CO2), and both emissions and atmospheric concentrations of CH4 have continued to increase since 2007 after a temporary pause. The relative importance of CH4 emissions compared to those of CO2 for temperature change is related to its shorter atmospheric lifetime, stronger radiative effect, and acceleration in atmospheric growth rate over the past decade, the causes of which are still debated. Two major challenges in quantifying the factors responsible for the observed atmospheric growth rate arise from diverse, geographically overlapping CH4 sources and from the uncertain magnitude and temporal change in the destruction of CH4 by short-lived and highly variable hydroxyl radicals (OH). To address these challenges, we have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to improve, synthesise, and update the global CH4 budget regularly and to stimulate new research on the methane cycle. Following Saunois et al. (2016, 2020), we present here the third version of the living review paper dedicated to the decadal CH4 budget, integrating results of top-down CH4 emission estimates (based on in situ and Greenhouse Gases Observing SATellite (GOSAT) atmospheric observations and an ensemble of atmospheric inverse-model results) and bottom-up estimates (based on process-based models for estimating land surface emissions and atmospheric chemistry, inventories of anthropogenic emissions, and data-driven extrapolations). We present a budget for the most recent 2010–2019 calendar decade (the latest period for which full data sets are available), for the previous decade of 2000–2009 and for the year 2020. The revision of the bottom-up budget in this 2025 edition benefits from important progress in estimating inland freshwater emissions, with better counting of emissions from lakes and ponds, reservoirs, and streams and rivers. This budget also reduces double counting across freshwater and wetland emissions and, for the first time, includes an estimate of the potential double counting that may exist (average of 23 Tg CH4 yr−1). Bottom-up approaches show that the combined wetland and inland freshwater emissions average 248 [159–369] Tg CH4 yr−1 for the 2010–2019 decade. Natural fluxes are perturbed by human activities through climate, eutrophication, and land use. In this budget, we also estimate, for the first time, this anthropogenic component contributing to wetland and inland freshwater emissions. Newly available gridded products also allowed us to derive an almost complete latitudinal and regional budget based on bottom-up approaches. For the 2010–2019 decade, global CH4 emissions are estimated by atmospheric inversions (top-down) to be 575 Tg CH4 yr−1 (range 553–586, corresponding to the minimum and maximum estimates of the model ensemble). Of this amount, 369 Tg CH4 yr−1 or ∼ 65 % is attributed to direct anthropogenic sources in the fossil, agriculture, and waste and anthropogenic biomass burning (range 350–391 Tg CH4 yr−1 or 63 %–68 %). For the 2000–2009 period, the atmospheric inversions give a slightly lower total emission than for 2010–2019, by 32 Tg CH4 yr−1 (range 9–40). The 2020 emission rate is the highest of the period and reaches 608 Tg CH4 yr−1 (range 581–627), which is 12 % higher than the average emissions in the 2000s. Since 2012, global direct anthropogenic CH4 emission trends have been tracking scenarios that assume no or minimal climate mitigation policies proposed by the Intergovernmental Panel on Climate Change (shared socio-economic pathways SSP5 and SSP3). Bottom-up methods suggest 16 % (94 Tg CH4 yr−1) larger global emissions (669 Tg CH4 yr−1, range 512–849) than top-down inversion methods for the 2010–2019 period. The discrepancy between the bottom-up and the top-down budgets has been greatly reduced compared to the previous differences (167 and 156 Tg CH4 yr−1 in Saunois et al. (2016, 2020) respectively), and for the first time uncertainties in bottom-up and top-down budgets overlap. Although differences have been reduced between inversions and bottom-up, the most important source of uncertainty in the global CH4 budget is still attributable to natural emissions, especially those from wetlands and inland freshwaters. The tropospheric loss of methane, as the main contributor to methane lifetime, has been estimated at 563 [510–663] Tg CH4 yr−1 based on chemistry–climate models. These values are slightly larger than for 2000–2009 due to the impact of the rise in atmospheric methane and remaining large uncertainty (∼ 25 %). The total sink of CH4 is estimated at 633 [507–796] Tg CH4 yr−1 by the bottom-up approaches and at 554 [550–567] Tg CH4 yr−1 by top-down approaches. However, most of the top-down models use the same OH distribution, which introduces less uncertainty to the global budget than is likely justified. For 2010–2019, agriculture and waste contributed an estimated 228 [213–242] Tg CH4 yr−1 in the top-down budget and 211 [195–231] Tg CH4 yr−1 in the bottom-up budget. Fossil fuel emissions contributed 115 [100–124] Tg CH4 yr−1 in the top-down budget and 120 [117–125] Tg CH4 yr−1 in the bottom-up budget. Biomass and biofuel burning contributed 27 [26–27] Tg CH4 yr−1 in the top-down budget and 28 [21–39] Tg CH4 yr−1 in the bottom-up budget. We identify five major priorities for improving the CH4 budget: (i) producing a global, high-resolution map of water-saturated soils and inundated areas emitting CH4 based on a robust classification of different types of emitting ecosystems; (ii) further development of process-based models for inland-water emissions; (iii) intensification of CH4 observations at local (e.g. FLUXNET-CH4 measurements, urban-scale monitoring, satellite imagery with pointing capabilities) to regional scales (surface networks and global remote sensing measurements from satellites) to constrain both bottom-up models and atmospheric inversions; (iv) improvements of transport models and the representation of photochemical sinks in top-down inversions; and (v) integration of 3D variational inversion systems using isotopic and/or co-emitted species such as ethane as well as information in the bottom-up inventories on anthropogenic super-emitters detected by remote sensing (mainly oil and gas sector but also coal, agriculture, and landfills) to improve source partitioning. The data presented here can be downloaded from https://doi.org/10.18160/GKQ9-2RHT (Martinez et al., 2024).

54 ENVIRONMENTAL SCIENCES↗